What has to be remembered here is that no system/component is ‘better’ than another. It’s all down to the subjective opinion of the listener.
If the OP prefers the SN3, then I’d suggest taking the win by returning the new kit, depositing the money back in the bank and carrying on enjoying the music.
I had the same system,252/300, for years and I’ve never had a low end issue. Have you tried to remove the Isoacoustic from your 252?
Relaxing the Burndy is important. I had a similar issue when I first got my NDS when I temporarily had its PSU further away. Relaxing the Burndy sorted it out for me. A picture of your stack would help a lot also.
It may be as simple as needing to warm up. I cannot speak for the 252, but the 552 definitely needs some time to warm up and settle after being switched off for any lengthy period. I reckon it takes ~8 days to give of its best (that’s just powered on and used occasionally, not continuous as some advocate, above). So I would leave it powered on and be patient before jumping to any conclusions.
The 252 needs some space around it. If you plonk an NDX2 on top of it, even if separated with IsoAcousics - which won’t necessarily improve things anyway - it’s hardly surprising that it’s not performing at its best.
252/300 really does need some care when setting these up, decent stand…ideally two. i would take away any none standard cables/isolation. also get some space around the 252. all burndies need to be off the floor aswel
Getting the right sound for you has so many factors- personal preference/room interaction and system synergy for example all make it such a personal thing.
I hope whatever option you end up with whether it be sn3 as a pre-amp with power supply and 300 or if you find with work the 252 improves or even if you try a 282 instead of the 252 and like that, that you end up happy with your system.
The 252 needs some time to settle down so it could take two to three weeks. I was surprised how my (used) suddenly got better after this time. The major change was bass definition as I recall.
You now have a lot of Burndy cables to contend with so some tinkering is often needed.
I’d pay some attention to the Burndy / SNAIC dressing if you can as this seems to have some impact. Lots of discussion on this Forum if you search for it.
You may also benefit from trying the Powerline Lite cables on everything if you have them. Sometimes expensive upgrade cables can add too much to the weight of bass frequencies. It’s worth a try and will cost nothing.
Both the 252 and the 300DR will inevitably add bass weight and the combination of the current mains cables / speakers and room may have tipped the balance slightly so swapping the cables may be beneficial in that respect.
The 252 is a great preamp and once you get it set up correctly, I’m pretty sure you will love it.
There are a lot of variables to play around with , so some patience and perseverance may be needed.
SL interconnects and DIn / XLR cables may assist in the future but my gut feeling is that the mains cables / Burndy dressing and the magic burn in dust which comes along after a few weeks will assist!
Hope you get it sounding like it should!
Thanks so much for all the replies so far. I am rethinking placement today and will follow advice from here. An important update, I spoke to the dealer who actually estimates that this system has run for a total of around 50-60 hours since purchase. It was not left running and was only turned on when a client requested a demo of the 252, which also makes me think that this dealer does not really understand the brand. I am taking this estimate with a grain of salt but it does make me feel much better, as this may now become largely a burn in issue. I checked back in today and things sound slightly improved, soundstage wise mostly. Not quite on song yet though, likely ways to go.
If it’s barely used, that will make a massive difference. It can take weeks rather than days of use to come on song from new. The set up of a 252 needs to be done right. If it’s not then you won’t get the best from it.
You need proper racking or very least separate shelves between the components. At this level of kit and in particular with the 252 you need to get the set up spot on.
Once you have the set up right and the 252 burned in you will be listening to a different preamp and set up.
It doesn’t sound like your dealer has helped you or explained this to you. It’s a good job you have us on the forum now to help you.
Like others have said, show us pics of your set up. We are here to help you.
With a Naim system if this level, correct setup is crucial. As a minimum, you should aim for a dedicated equipment rack with a separate shelf for each box, especially the preamp. If you can’t accommodate that, it’s possible that the Supernait is a better choice for you.
I’ve always felt the SN3 has much better speed than 282/250DR and 252/300DR, so it’s not just you who has that opinion. Going to separates in the classic gear gives you much more in other departments. The New Classic gear solves this problem.
Yes I heard this too when I had a SN3 next to my 282/250DR
Then I realized because there’s a lot less bass in the SN3 compared to the 250 Dr !
I went from SN2 to 252DR/300DR and it was a substantial upgrade. However, as others have advised it needs some time to sound right, even if it was well used I’d give it a week or two switched on. It initially sounded thin and overly analytical to me but this eventually settled into a more relaxed presentation. If anything, one of the biggest improvements for me was soundstage so plenty of run in and care with set up should be prioritised before making a judgement.
As others have mentioned, just in general as you move well up the ladder, all the small details matter if you’re wanting to achieve the level of performance the kit was designed for. Number of good things to start with have already been posted. Have you tried without the ISO acoustics footers? I have never tried them under a Naim component but I did try them under my current DAC & didn’t like what they did, they bloated the mid bass.
Couple thoughts, have never owned/recall hearing a Supernait but the new combo will be far more transparent & the SN might have been artificially enhancing things. I have not heard your speakers, but the first word that comes to mind with Dynaudio would not be speed & being their called a heritage special, I would think they would be more of a “vintage” sound? Maybe the SN was compensating for this while the 252 is just revealing how the speaker should actually sound?
As per advice on here, all components are on separate shelves and no signal cables are touching the floor. I have removed the isos. Currently on day 5 and the system has started changing significantly. The 252 is much more analytical than the SN3 I agree, there’s a lot of extra detail that is being retrieved with the 252, and now the soundstage has started opening up. SN3 is still more pratty as of today. This is evident with my dynaudios which are actually some of the fastest transducers I have ever experienced (I very much agree with Steve, see here: http://www.stevehuffphoto.com/2021/02/17/the-dynaudio-heritage-special-speaker-review-worth-the-7k/). However, going back to the SN3 from the 252 now feels like a significant downgrade. I think that once bass tightens a bit more, the SN3 will be in need of a new loving home.
Great news, nice to see you making progress.
Sounds like everything is coming on well for you. I have no experience of the OC separates but did have an NDX2/SN3. As good as they were, I assumed the OC separates would be superior which is what you are beginning to find. I am glad that I swerved the OC and changed to NC. They sounded great straight out of the box and instantly better than the NDX2/SN3.
The clever advice on here points towards patience and burn in - hopefully all will come good for you soon. Good luck.
Plot twist.
Today I was playing with the balance pot to get the channels at matching volumes, hoping it would help with my soundstage issue. I fired up the channel selector in Roon so I can easily switch between left and right from my seat. Switched to left channel only in Roon, and… both speakers playing at lower volume. Switching to right channel only, same result. Switching to both channels, volume gets louder. What the heck?!
Now I’m in panic mode and trying to identify the source of the issue. The balance pot on the 252 works fine to isolate left and right channels, so it’s not the 300DR. The NDX2 works fine with the Roon channel selector on the SN3 so it’s not the streamer. Turns out the culprit is the 252! Even when using the RCA inputs, and yanking the cable from one channel, both speakers are still playing audio! I am now thinking this is going back for service, and searching for any mention of the same issue on this forum, with not much luck. But wait, let me first try one last thing. I go into program mode, reset to factory defaults and… wow. Channels are working properly now, the soundstage is 3D again, the low end is tight and visceral and SN3 is eating the 252’s dust. On song at last 
Great news. When something sounds so obviously off it’s usually something fundamental. Now you can obsess about fine tuning knowing the basics are right. 
Glad it worked out for you.