#1 Alor no contest but could be quite touchy end of december : bucketloads when it rains.
Alor has way more variety in dive sites, but in my limited experience has fewer of the really strange creatures you can find at Lembeh. However, I have done dozens of muck dives in Lembeh and only 4 in Alor so…
This year the macro was pretty bad in Alor, I had very few critters in August on a few dives in Kalabahi bay.
On a regular year it's one of the best places in Indonesia for rhinopias sightings (this year Tulamben in Bali was/is still overcrowded with them).
I've already seen Hairy and mosaic octopus, lots of froggies, various kind of shrimps (Coleman, harlequin..) or nudis (Phyllodesmium, eubranchus, marionia sp.) in a good year. It seems they are very seasonal or yearly dependant in Alor more than anywhere else.
Currents are something typical in Alor but a good operation who knows exactly the tides and sites configuration will always manage to deal with less currents (unless you need some). That's why it is preferable to dive Alor with resident resorts than with liveaboards who are less accustomed with Alor divesites.
Lembeh is great for black sand macro. However I understand it can be boring if you're not into that (even for me, macro photographer, I can't stay more than a week in Lembeh)
Palawan is certainly not the best dive spot in PIs. Why Palawan???