I recently watched Temple of Doom again for the first time in years. That one has always not seemed to fit in the trilogy for me. It's still a good time, but it's the weak link in the Indy chain, for me at least.
A few things about TOD that bother me:
1. They made Indy appear to be more of a mercenary than an archaeologist, or one who fought to preserve artifacts. The movie open with Indy trading the remains of the first emperor of the Manchu dynasty for a diamond. Huh? Indy was treasure hunting for hire? The Indy of Raiders and Last Crusade would not have done that.
2. The movie relied a bit too much on sight gags. The whole dinner scene with "snake surprise", etc. was overdone. Raiders had some gags, but they were incidental to the action (classic moment in the market where Indy shoots the swordsman). In Doom, it felt like the action was trying to set up some of the gags (Crusade was somewhat guilty of this as well).
3. The "bug" scene pales in comparison to the snakes in the Well of the Souls (and was not as good as the rats in Crusade).
4. The Shankara stones were just not an effective artifact. There was no build-up to the moment when their power was really revealed. The Ark in Raiders was perfect. The whole movie built up to the point when the Ark was opened and its power was releaed. The Grail in Crusade was not as good, but the scenes where Indy has to avoid the traps to reach the Grail room, and has the confrontation with Donovan and the Knight in order to heal his father were still effective. Doom has the very cool rope bridge scene, but that was just a daring escape, rather than a revelation of the Stones' power. Afterwards, you find that the return of the stone has "brought life back" to the village, but it just doesn't hit you like the Angel of Death being released from the Ark.
5. The set up of the movie took a long time. After the initial brawl in Shanghai, the pace of the movie really slows down. You're almost an hour into the movie when Indy finally discovers the Thugee temple. The rest of the movie then moves at a breakneck pace.
6. Mola Ram was not a great villian. This is mostly related to #5, because it just took too long to introduce the character. Certainly couldn't compare to Toht from Raiders. Donovan in Crusade was so-so, but Crusade also had the interesting twist of Indy's love interest betraying him.
Some of the above is nit-picking. I still liked the movie. However, Raiders was so pitch-perfect, that Doom just doesn't stack up very well against it. Crusade fares much better. It was closer to the tone of Radiers, although still got a little too slapstick in parts. The action sequences also couldn't compare to Raiders. Sean Connery as Indy's father, however, made up for a lot of the movie's shortcomings.