If those are games that have to be installed or have big save files, it could be the case that your hard drive is fragmented. You could try running a backup, formatting the drive, then restoring. If you've got a way to plug a hard drive into your computer, you could also defragment it from there. There's also a rebuild database option in the recovery menu, but I think that's more to do with the XMB than the drive itself. Could be worth trying.
I don't think it's a CPU or GPU issue -- even if your PS3 is running hot, I don't think it will ever underclock itself, because that's counter to the way consoles are assumed to work by developers. If this isn't a hard drive problem, it's likely that's just how those games are. I don't follow this stuff that closely, but more often than not, the PS3 versions of games seem to not perform the best.
No matter what you do, back it up first.
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