There's no input lag to speak of on Mini 1st gen, iPad 2 and iPad Air. Don't know about other devices, sorry, tho I've never seen that mentioned before. The game will either run buttery smooth at 60fps locked with perfect response times or be messy like I explain below: it's not like even when it runs fine you can also experience input lag.
On Mini 1st gen (and at least also on iPad 4th going by your post) there's a problem with stuttering tho, which is probably what you're experiencing, were the game craps out and becomes a 15fps stuttery mess: you'll notice it straight away as soon as Commander Video enters a level; after the update it can be fixed by simply exiting out of the level and going back in (it's pretty straightforward), they've acknowledged the bug tho (which I also point out in my post) and working on an update coming soon (as per their twitter feed @BitTrip). The problem will usually come up when your wifi/3G gets spotty/drops momentarily (like I was saying to Mario a few posts before) or you earn a GC achievement, probably related to a memory leak especially when there's "talk" between the game and the device's dormant apps/features.
Since the last update the port's performance has increased ten folds, it's safe to recommended it in my opinion.
Of course, as I've mentioned, if an update wasn't coming then I'd be less lenient but I'm super picky about framerate and response lag and luckily it's pretty quick to go out of the level and then back in.
We should ask Mario, or other devs who post itt, but my guess (just a guess!) is that if it were a "real" widespread memory leak I don't think you'd be able to fix it unless closing the app, which isn't the case here since you get to run it in a perfect state again while always staying in-app.