I completely agree with your comment that i would much prefer to dive a good dive site many times, rather than go to a mediocre location for new dives. I have dove the liberty wreck in tulamben probably 10 times, but I once got in the water before 6:00am and it was a completely different dive. White tips swimming by, schools of humphead parrotfish and most importably, not another sole in the water, it felt like a new dive, especially because the light was different as the sun was just coming up.Bali has more infrastructure(pro) - more tourism (con).
Mlpscua has great atmosphere, laid back people, no aggressive touts, great variation of diving (but some is 'advanced' when the current is running.
My money on Mpascua. 2 weeks for me there is about right.
Some divers don't like visiting the same sites. These people often talk about 'doing Thailand' or 'doing the Great Barrier Reef'. In reality, diving the same site (even hours apart) provides a unique angle due to sunlight/current/profile etc. I quite enjoy diving 3-4 times on the same site for this reason; you get to 'know' the site and can modify your approach to make it better each time. I'm also in to u/w photos so I consider that when wanting to get the 'perfect shot'.
I would have to disagree with your comment that the currents make diving more challenging in malapascua. I would consider Bali more challenging diving, but with both I guess it depends where you are diving. Tulamben may be very easy, (although I always hate that entry on the rocky beach), but Nusa Penida has currents that can really move. Malapascua seems much easier to me (atleast the week i was there), although Gato Island could get a decent current.