I am not one of those that complained, although I can see that it is annoying when a game gets too long, especially when this game has flaws. Some flaws are much more tolerable for a 10 hours game than for a 100 hour game for instance. For example if the loading times are long, but you're playing 10 hours, you'll spend in total maybe 10 minutes in total at long waiting times, which is bearable. Buf if loading times are long in a 100 hour game, you'll have to stand 1 hour and 40 minutes in total at waiting times, which is unbearable (even though they're not longer than in the short game with the same loading times).
Same could be said at other flaws, the loading times is just an example that came to my mind. For example if the enemies aren't varied enough, or the combat system is good but too simple, or that the game is too easy, you won't be bothered by those flaws in a 10 or even 20 hour games, but you will in a 100 hour game.
Another reason is that people often have a large pile of games they'd want to play but limit how much they play simultanously otherwise it becomes a mess. Long games tends to monopolize the waiting queue and prevents to start a new game that you are waiting to paly. Of course it does not actively prevent it, but you know from experience that if you start yet another game, you'll necessarly abandon one of the game you started to play without completing it.
So if you're not a complextionist and don't care leaving lots of games half-finished, there's really no bad side in long games, but if you're a complexionist, it can become an annoyance.
Last but not least, if a game is really that long when you finally finish it, you are more likely no never replay it ever again (or at least not fully). However if a game is short, then you can pick it up every 3 years or so and finish it within a couple of week/months, which is nice. (Chrono Trigger comes to mind here).