While I agree with your stance on Bender's Big Score, the Beast With A Billion Backs was absolutely fantastic. It didn't rely on injokes to the extent the first movie did, and once you get past the fact that the tentacle monster talks with the voice of David Cross, it shines out as one of the best Futurama moments to date. It's up there with The Series Has Landed, Jurassic Bark, The Luck Of The Fryrish, Leela's Homeword, Parasites Lost, The Why of Fry, The Sting and The Devil's Hands Are Idle Playthings. More so than any of the other movies, it fit in perfectly with the weirder moments of Season 4, being a little crazy and strange while simultaneously being really touching, though perhaps not as involving as some of the previously mentioned episodes.
I think Futurama, the movies more so than the show, can be divided in to the categories of 'plot driven' and 'character driven'. For me, the show was at it's best during the character driven episodes, that relied less on gags and more on character development and interaction. I think this is the big distinction to be made between the first two Futurama movies.
While they're back to back sequels, with the second picking up where the first left off, their approach is drastically different. So, what they did with the second movie, that really worked for me. Initially I was a bit weirded out by some of it, but once I started to recall exactly how weird the show got sometimes, anything that happened in tBWaBB seemed tame by comparison.
While the first movie was crowded, the second movie was more or less exactly what Futurama always has been, albeit more developed and realised. Far more focused than the first.
The movies are so haphazard. Some of the strongest Futurama moments to date interspersed with some of the weakest. Alas! You must take the good with the bad, and any Futurama fan owes it to themselves to view these movies, each of them, in order, allowing them to draw their own conclusions. Don't worry about tainting your memories of the show with substandard movies. The movies are exactly what the show always was. Just, prepare yourselves for the third movie because boy are you going to be disappointed. I'd say skip it, but outside of the terrible parody aspect, it does have a few important plot points and character revelations you might need to be aware of for future episodes and some redeeming features. Namely, all the scenes that take place outside of the fantasy world that takes up most of the movie.