They're both going to be very nice lenses overall assuming both are in good condition. You're probably going to love any 50mm/55mm/60mm macro from the era, really!
There are a couple slight variations of each, I think. Some 55/3.5 Micro-Nikkors have an aperture compensation mechanism to account for light loss, some don't. Some are optimized for close-up work and thus suffer slightly at far distances, some are a little more balanced. There's a preset Macro-Takumar that focuses natively to 1:1, while later Super/Super-Multi-Coated Taks did 1:2 and came with an extension tube for the rest.
I did once compare a Micro-Nikkor 55/3.5 (infinity to 1:2 natively) to a Sigma 50/2.8 (infinity to 1:1 natively) and a preset Macro-Takumar 50/4 (the one that does go to 1:1 natively). I liked all of them. At the time I was trying to figure out which one to keep. In the end, I made a utilitarian decision to sell the ones that would net me the most cash; the Nikkor and the Takumar... Today, I have regrets!
I still have/use/enjoy the Sigma (and accumulated a few other samples/versions (AF on EF via Sigma MC-11). I have since also re-acquired a Nikkor (different version though hehe) because it popped up very cheap locally. Given the same opportunity I'd definitely grab the Macro-Tak again.
https://www.dpreview.com/forums/thread/3991052
The Micro-Nikkor 55/3.5s I have used tend to have red/cyan color fringing, while the Takumar's color fringing was more towards magenta/green but also more subtle. In my post-processing pipeline (Capture One -> Photoshop if necessary) I've found that lenses with red/cyan LoCA can end up being a little problematic in the pixel-peeping arena - I seem to get more democaicing artifacts (zippering, etc) with them and they come across as being a little less sharp (is this a Bayer CFA issue? Will it effect X-Trans? *shrug emoji*). I often find myself more distracted by red/cyan as well, but to be fair, the Micro-Nikkor was plenty sharp and takes excellent distraction-free B&W images.
The Macro-Takumar's aperture is a bit odd - it can make star shapes in the middle of the range, which I found interesting and charming, but tends to be more rounded wide open and fully stopped down. Strange aperture shapes are not everyone's cup of tea.
