I'll offer a slightly contrarian opinion.
IMHO, the magwell design is one of the highlights of the HK416/MR556 system, and I'm actually slightly disappointed that they "caved" (I know this is a gross oversimplification) on the magwell design with the HK416A5.
Besides giving the HK416 a distinctive profile, which is merely cosmetic, the 416's magwell is lightly flared/ramped, just enough to make magazine insertion a little easier, without being a huge funnel like something like some of the aftermarket magwells--it's obviously not a competition magwell, but it's a small, but nice touch, like many of the things that I like about the 416, where the feature, in and of itself is not a huge deal, but with other small improvements, adds to the overall "package" that you get with the 416 aside from just the piston, which is what obviously gets the most attention.
Also, and this is anecdotal, but according to another member here who has done a significant amount of weapons testing (on a large-scale, mainstream manufacturer level, not a cottage shop that does an occasional "torture test" for YouTube) that HK416 lowers would improve feeding and reliability for otherwise problem uppers when used with standard M16/M4 style lowers. I don't know exactly what, if any "magwell magic" HK did when developing the 416 magwell, but I do know that they tweaked the HK416A5's feed angle by about a degree to half a degree to further aid in feeding and reliability, and I would not be surprised if there are other small dimensional tweaks in the legacy magwells besides the flared and beveled magwell opening.
Besides that, the stock MR556 lower comes with "match" receiver pins that supposedly remove slop, but require a tool to remove--I am not a fan of these, but they're a difference. I have replaced mine with standard AR pins.
The FCG is also a distinctive design, again, it is a "match" FCG, but the HK FCG allows you to put the weapon on "safe" with the hammer forward. Another feature I neither want nor need--but again, a difference between the MR lower and an AR lower.
Finally, the buffer retainer design, while a fairly small improvement is, IMHO, an improvement nonetheless. It is held in place by a roll pin, and has a large "blade," rather than the standard AR design that is held in by the timing/depth of the receiver extension and has a rounded, tapered "tit" that can eventually chew up buffer faces, and have on some occasions come loose, popped out, or simply broken off inside rifles (yes, I am aware that in a perfectly functioning gun, the BCG is supposed to keep the buffer off the retaining pin--this does not mean these things have not happened before).
Regarding magazine compatibility... I honestly and frankly see this as a non-issue--just don't use pre-M3 PMags in the HK lower. I don't dislike PMags, and have used and own PMags of every generation since Gen. 1 in 2007--I even have a spare Gen. 1 body left over somewhere from the very first PMag recall. I understand that some folks have "standardized" on PMags and have stashes of hundreds of NIB M2 PMags... the vast majority of my magazines are still USGI aluminum, and it's not as though it's hard to distinguish between them. With the M3 PMags, it's a non-issue anyways.
Ultimately the HK416 was already designed and in service when the PMag was introduced--it's not as if HK designed a gun that was incompatible with the PMag as some sort of "fuck you" to the aftermarket as many seem to believe.
Now... all that being said...
The current "market price" for "loose" MR556 lowers is absolutely, General Butt Naked-level insane. There is no reason that an MR556 lower is worth that much except for some folks believing they're forged with magical Teutonic fairy dust, and it's absurd that used MR556 lowers are sometimes bringing more than used MR556 uppers.
As for what to do with your upper... if you can find a deal on an MR556, I think they're worth grabbing, but as the prices on them continue to go and stay up, it becomes increasingly unlikely.
If you're not super attached to your MR556 upper, and simply can't live with it without an MR556 lower, then I would sell it before paying the market price for an MR556 lower--you will not "add" enough value by bringing the upper and lower together to justify the cost of the lower alone.
At the same time, if you've got money to burn and an MR556 upper you're uncertain about--I would recommend getting it cut down and reprofiled, you may end up liking the upper way more than the stock, factory MR upper--a cut and reprofile job will vastly improve the balance and handling, and it will feel like a brand new gun. Also, as long as you stick to "traditional" factory HK416 profiles and barrel work (not weird, niche lengths/profiles/etc.), they will hold their value fairly well, even after being chopped and reprofiled, as there are many folks who want to build HK416 "clones," and will buy a "turn key" MR556/HK416 conversion for a decent price.
~Augee