While it's more the mechanics that annoyed me with the latest FU version, one thing I've always felt is that FU changes the Starbound art style and general themes too much for my tastes.

Biggest case in point: the Shoggoth mission. It's extremely bloody and gory, something which is completely absent from vanilla Starbound. Personally I'm not a fan of mixing art styles together without a REALLY good reason why (e.g. Crossover-related mods/games), and I feel that the pixelated blood and gore and gibs just doesn't jive with Starbound's base graphics. The Precursor object and block graphics don't feel like they fit in all that well either, feeling like they were imported from another pixel art game and didn't get enough tweaks to fit with Starbound's art style, though it's still less problematic than the blood/gore above.

There's various other FU-exclusive additions that don't feel like they truly "belong" in Starbound, too. Several unique monsters added by FU were at one point using placeholder graphics from other games, though I believe they're now using unique graphics. Problem is, they still don't really feel "Starbound-ish".

I don't really know how to explain it in a concrete way, but the art style conflicts really hurt FU imo as it never really feels like a true extension of Starbound and more an entirely different game slapped into the Starbound engine, but keeping the original assets anyway because why not?

Other main beef is with the new Research system and how it takes EONS to get past Titanium-tier gear. I get that it's supposed to encourage exploration, but it really bogs things down when you have to be ♥♥♥♥♥♥♥ around on high tier planets for hours before you get everything necessary to make all the gear needed for Tier 4 and beyond, but tbh that can still be tweaked; the art style conflicts are significantly more ingrained into the core of FU, and thus much less likely to be "fixed" officially any time soon.