I am really enjoying working through KO2001. The heavy review with gradual adding of new kanji seems very effective.

I am getting towards the end of the 1st book and will probably move onto the second but I am thinking long term about something post KO2001. KiC looks good but it uses the older Joyo Characters and I would ideally like something which takes into account the 2010 revision characters. Does anyone have any ideas?

Wouldn't it be more effective to try to tackle native material afterwards? I mean, someday it's going to become a relevant topic, might as well not stretch it out for too long.

Im doing native material also, just simple stuff at the moment but I really like how KO2001 gives you 3 or 4 sentences with lots of examples for different readings, the constant reinforcement works really well for me.

Just do KiC? Afterwords you can look up the leftover kanji on your own and use example sentences from a dictionary (there are lists of the changes in various places)

The fact is that learning absolutely every joyo kanji isn't very important. If you understand 95% of them you'll be doing just fine, which is what KiC will still accomplish despite the changes.