Like many others, I want to pass kudos on to the dev team on the planner. I've been recommending it everywhere (Gen Chat, Guild, Steam forums, you name it) for several years now, because there's nothing else that comes close. Thanks for doing this.
As for suggestions, my first is for feats:
I often like to work from general to specific (I think they call that 'global thinking'). In build-planning, that means that I like to develop a 'pool' of the feats I'm considering for the build with no consideration of levels, prereqs or anything else. Then I select from that pool when actually assigning feats to levels. This intermediate step brings the feat list down to a manageable size (usually less than two dozen contenders). Probably the easiest way to populate the pool is by having checkboxes beside the feats in the overall list. Then it would require the ability to 'show only selected feats'. Clearly this is about supporting a particular creative process, but I think it might not be an uncommon one.
My second suggestion is about enhancements. I gather that to a large extent, you plan to simply recreate the existing Enhancement Planner, and since its functionality is exactly like that in-game, that's near-ideal. The only thing I would like added is kind of a 'what-if' option. Sometimes when I'm planning a multiclass, I know the primary, but I'm considering various possible secondary classes or even on a pure I'm not sure which race will work best. Working from the same 'general to specific' creative model I mentioned above, I want an overview of the enhancement trees of possible races and classes so I can decide which to take. Usually I'm doing this before I've picked how many levels of which class, let alone at which levels I'm taking them. I'm not so much selecting enhancements as looking at what's available. In this mode, I'd prefer to see what all three tiers of an enhancement grant simply by hovering over that enhancement (and without consideration of prereqs.. neither enhancement, feat nor stat). Having to change races/classes/levels in the main screen simply to see this information is painful. I think that this would be best set up outside the current enhancement selection window as a button on the main screen that would open a modified Enhancement window that would allow selection of race/class/class/class, not bother with level considerations at all (treat all as L20), and allow no input (simply show all tiers of tooltips for the enhancement the mouse hovers above). No information from this screen would be used to populate the actual planner. You would want to retain the race/class selections chosen here during the planner session (to allow revisiting), but need not save them at all.