I myself levelled healer tree to rank 4 to get choco cure, since it is a lot better than choco regen (for chocobo to use cure it has to be in healer stance though), and then levelled tank tree, since I did not care to get barding as soon as possible. Just choose whatever is most useful to you while you are levelling.
Do not bother feeding krakka roots while chocobo is low level, it is a waste of gil (or your time, if you are growing krakka yourself). Just take him with you wherever you go. Make sure to complete companion challenge log. At low level it does not seem much, but later you can get 300k and more exp every week just from the log.
