It's a bit difficult to explain and to put in words, so bare with me cause I'm still thinking on how to best word it.
I have no issue with the Abe Lincoln references in FO3. That's just one example and at least with DC, there's quite a few museums regarding American history (to my understanding. Got family there, never been myself). I also would have no issue with the Minutemen as a lone example.
The cause for concern is just a pattern of Bethesda's writing, with the muskets suggesting their writing hasn't improved. In FO3 they did rely heavily on the whole "'MURRICUH" thing alongside the 1950's. The "'MURRICUH" aspects I'm ok with because again, if there's a city to do those aspects with, it's D.C..
My worry is more that Bethesda does not know how to do anything else. My worry is that they have no original thoughts in their heads, so copy-pasting history is their go-to method for writing. It's not so much that seeing groups like the Minutemen or the Kings is a bad thing in and of itself, but rather if it happens super frequently, then I'd consider it a smoking gun for stupid, uninspired writing. History as an inspiration can be great. Caesar's Legion is a testament to this. Josh Sawyer himself is a history major, so whether you realize it or not, there's actually quite a few historical references alluded to within New Vegas' writing, but it's done in a rather intelligent way that isn't so....blatant? Obvious? It's subtle, well thought-out and planned. Regardless, the groups themselves with historical inspiration are not the issue.
The issue is merely that if all Bethesda is capable of doing is copy-pasting history, then I do not have high hopes for the writing. I'd expect it to be predictable, more focused on making references rather than making SENSE of the references, and like it would get very old very fast.
Just for comparison? In Oblivion, the enemies were far less impressive and inspired than Morrowind. Morrowind was truly alien; everything we saw there was new and different. It was a world with giant fungi, giant insect-like creatures we could use for transportation and...giant floating...jellyfish things. Nothing about Morrowind's setting said "I was inspired by this." It all felt new and fresh. It was so new and fresh that honestly I think Morrowind's setting could be a bit off-putting for some people because it was just that alien to them.
Then came Oblivion. Oblivion had enemies we were familiar with. Ogres, Minotaurs, Bears, ghosts....all the stuff you'd expect from the typical fantasy setting. I noticed this and thought they probably did it conciously and on purpose for the sake of tying the home of men (Cyrodiil) into more traditional fantasy concepts. I thought it was clever.
Then came Skyrim....it wasn't clever. It was them being uninspired. Again we got ghosts, bears, sabre cats and other traditional concepts. One could argue that's because Skyrim is again a land of men, but I would question if Skyrim wasn't purposefully chosen because it allows for lazy writing. I would question if the next location won't be Hammerfell or High Rock just because it'd allow for more of the same.
And now I find myself recognizing that FO3 had "'MURRICH" themes to it and I thought it was fitting given that the city it took place in was D.C....but what if it's not a concious decision in regards to D.C. and instead it becomes all they know how to do?
Tl;dr
There's nothing fundamentally wrong with groups that reference history. There IS something wrong when you overdo any theme, historical groups being one such theme. Seeing a historical group such as the Minutemen follow their concept to the point where it's downright counter-intuitive (they use obsolete tech and seem to have little armor) suggests that Bethesda isn't focused on making historical references be solid, working ideas, but rather that referencing history might be their go-to and they don't really know how to do anything else, which would be a huge smoking gun that the writing will possibly svck.
http://fallout.wikia.com/wiki/Recharger_rifle
Uses no ammo, charges automatically over time, is honestly a piece of crap, yet it still fires much faster than the musket. The best variant is the MF Hyperbreeder Alpha, which charges much faster than other Recharger pistols to the point where it's practically an SMG that needs no reload and very few pauses, or a pistol that will never need a reload.