If there's a time pressure (ME1 tried to do this, although the minigame was dumb and poorly explained) then I think it's a lot better. If, for example, failing to open the lock meant it was jammed forever, then the minigame means something. It's the minigames that do nothing except force you to play the minigame until you win that I have a problem with. The punishment is more shitty minigame, rather than lost loot, hps, or whatever.
A skill check is fine too, as long as the skill in question has realistic viable reasons not to take it. If it's like fallout, then you are stupid not to take the skills to let you open doors and hack computers, so those are more of a character level check than something some characters would have access to and not others. If fallout had enough worthwhile skills and perks such that it was reasonable not to take the hacking or lockpicking skill in some cases, those skill checks would be a lot more meaningful.
I loved the oblivion lockpicking minigame... for the first 10 times or so. Of course since you had practically infinite lockpicks after very early game, it just became an annoying waste of time.
As I said before, I think the Deus Ex hacking minigame was pretty close to what a minigame should be, but they missed a couple of points. Just aborting when the security alert timer started getting low should not have worked, you should have gotten an alarm in that case. Plus, saving should have been restricted to some degree so you couldn't just savescum them, but that's a much bigger issue than minigames in general (although it is very relevant, a fail condition doesn't matter if it just means you reload and spend 30 seconds looking at a loading screen).
The biggest issue with the various minigames like this is the punishment for failure is typically more minigame, rather than any consequence in the main game itself. Nobody ever got locked out of a computer in fallout, nobody ever ran out of lockpicks and couldn't get that sweet treasure in oblivion.