Personally I would do at least +7 days just in the Galapagos. I've done a 2 week extension at least a couple times. If you're keen to dive more I've had some great dives at sites that are now restricted to the land-based ops, e.g. my best frolicking sea lion dive at Mosquera, and my best schooling rays at Gordon's Rocks (admittedly both were done with liveaboards before the dive sites got split by GNP). I've done Kicker Rock twice with land-based ops and enjoyed it both times - one of the two days was absolutely superb (e.g. better than my Isabela liveaboard dives). My only concern would be dive time restrictions and potential 'babysitting' from the land-based ops. For Kicker Rock the issue is getting a dive op to confirm the trip, esp. if you are the only one who wants to dive it in your party. You need a local person to wrangle that and it may only be confirmed a few days before you land. You could also do a land touring cruise which visits sites you can't see any other way. Or there's lots to see in Isabela by boat, foot, bicycle, etc.
My experience diving Malpelo (Colombia) was far beneath my experience of the Galapagos, but I have only been there once. The other side of Colombia is Caribbean diving.
Cocos vs. Galapagos is IMO a religious issue. I far prefer Galapagos but again, some of that may boil down to luck. I would avoid Cocos in an El Nino year.
You could consider an Ocotal, Costa Rica extension. The non-fed bull shark dive there is eerie. But other than that dive, the diving is far below Galapagos IMHO. You'll have to book with Rocket Frog to make a bull shark trip in the winter (which also requires a 4 diver minimum). But is that one dive worth going all the way there? I would choose Galapagos wildlife over Ocotal personally, but I am not a partier.
You could consider some time in Corcovado National Park in Costa Rica. I have not been but have heard it's wonderful.
