I'm replaying through all of them up to A Crack In Time a second time. It's nice to be able to see these games through a critical lens. As a kid I guess I just implicitly thought Up Your Arsenal would be the best cause it was the 'newest', but I'm noticing it's actually a pretty weak entry. The online mode was fun, and I guess as I kid I just didn't notice how much the single-player took a hit. Still a fun game, though.
I'd say right now, probably the first one is my favorite. For some reason, it just feels like they put more effort into it than the others. The tone of the game seems quieter and more natural than the other ones. While I love the environments in each entry, it's the first one that felt like the environments and navigating them took a bigger part compared to blowing up robots. I also like Ratchet's personality in the first one, even though he was criticized for being kinda mean. The transition to a 'nicer' Ratchet in subsequent games feels a little muffled, like they're making him something he wasn't supposed to be.
I haven't played A Crack in Time or past it because it doesn't work on RPCS3.
Up Your Arsenal was easily my choice for best game up until A Crack In Time came out. I never played the online portion, but the story was fantastic and hilarious, there's a ton of worlds to explore, and the weapon upgrades felt great to pursue. My issues with most of the other games is they never hit the high bars set for content that these two had, and the story never seemed to hit the same highs either, either for UYA's humor or Crack's emotion.
Regardless, I think we can all agree that not getting another game for at least half a decade more really sucks.