You're supposed to use that time to think about YOUR next moves as well. Sometime you don't need to do that, but a lot of times you'll sense that there's something good hiding on the board that you can discover if you take the time to find it.
Once you play harder opponents and hit multiple very complicated positions in a game, you won't have time to do "deep thinks" on every move. So you use the opponents time as well for your own moves.
It's also training for playing in tournaments where, yes, you will possibly sit at the board for 3-4 hours with only short breaks. If you have the discipline to do that and the opponent doesn't, you'll win.
Keep a real board beside your computer and play off of that instead of staring at the screen.
Chessmaster rarely takes more than 5 mins a move. I've seen 15 mins with certain opponents who don't manage the clock very well, and they can only do that once or twice before they run into serious time trouble and they start moving faster.
Try 40 in 40 plus 20 for a quick longish game that's exciting.
The "normal standard" (which used to be 60 in 120 plus 60...I don't know if they changed it recently or not...that's a possible 6 hour game) is a little too long. I never train with that time. I want all games to take 3 hours max and average about 2 hours or so. It's a little tough to start the long games, but after about 20 mins or so I get really into it and it's almost hypnotic. It's similar to runner's high a bit and you really forget about any crap that happened during the day. It's actually very pleasant if it's a nice evening and I've got the door and window open and the sun streaming in shining on the board. I don't see it being much different than practicing a musical instrument a couple of hours every night or practicing anything else that you want to get good at.
You can also play longer games over several sessions by adjourning it. Play an hour a night or whatever you can manage and play a game over 2-3 nights. That's also good practice for sizing a position up quickly because you will find that you'll always make your worst mistakes on your first move after a break.
But honestly, I would just try to find the time that's right for you. Try game in 45. If you find that you're always in time trouble and you feel rushed, then bump it up. If you find you're never in time trouble AND you're always winning then move it down. Find the sweet spot where you feel that you are frequently losing games you should have won because you didn't have enough time and then bump it up a little bit. I wouldn't start playing super long games just for the sake of doing it.
The more you practice, and the more you learn the more time you will want on your clock, but playing G30/G45 against the 1000-1200 rated opponents is actually a good idea since they're not usually that tough to clobber quickly.