I also listened to the albums in order recently and noticed the same. The first album is the most creative and eclectic in many ways, and each album loses a little of that essence but the production values get noticeably better.
That said, my favourite is probably Lincoln which is nearly as crazy as the first, but with slightly better songwriting IMO.
I also love John Henry in a different way; the songwriting and production is as good as TMBG gets, but it definitely has a different vibe to the first two albums.
I find most post-90s TMBG albums get very much slept-on. I also love The Else and Glean, but again they have an entirely different vibe to the first couple of albums.
Post-90s their songs start to get a bit samey. There are definite stand-outs for sure, but the albums as a whole shift to a more homogenous alt rock.