It isn't just about finding missing gems or boos, it's that the mission based system harmed the flow of the game. With the original, I felt a sense of progress as I cleared rooms of both enemies and money. The lights of an area turning on after a boss fight and the (beforehand locked) door to the next area unlocking gave me a sense of accomplishment. The mini-bosses gave certain rooms that special charm they needed. The mansion felt huge and your step-by-step exploration of the areas only added more to the weight of it all.
With LM2 they're fairly small areas that you're going to have to visit over and over again, your room progress constantly resetting (aside from some obvious main objective changes, of course) and the mansion being full of constantly re-used baddies with barely any special enemies to counter that repetition.
It's not entirely about content either. Yeah, LM2 might have more things to do (aside from badly designed upgrades and whatnot) in terms of 'content', but its elements don't function as well as they should and in a cohesive manner. In terms of which game is better? I'm not sure, as LM1 was riddled with flaws as well. It's just that this game unfortunately did not live up to the high expectations I got from the praise and the high review scores. Mission based structure worked extremely well in games such as Kid Icarus and especially Fire Emblem, but it just doesn't work for me in LM2. I'm still enjoying the game and working my way through it, but I doubt it'll somehow manage to blow me away in the end.
I would have preferred if the constant, unnecessary returns to the lab were removed from the game and it instead took a design with better flow. Remove the mission-based system, make each area larger and let us play through the entire area. We'd still be completing the same objectives and E-Gadd could still keep us updated through the dual scream and we'd be able to transport certain equipment through the teleporter thingy without constantly having to go back. That said, if the game didn't force us to go back and replay levels, it would probably be over incredibly quickly. The game actually isn't that long, it's just made to feel this way because of the constant returns you make to the same area.
But it is true that the flow is broken up a bit more with the mission structure, but again I wasn't bothered since it seemed pretty justified; I like E.Gadd's dialogue and I like coming back with the spoils, gradually upgrading the poltergust and storing all them busted ghosts. 
