We can never be sure with “counter-factual” history, but my best guess is that very little would have changed in terms of the Philippine-American War. Luna may have been the best Filipino general, but (1) he was still inexperienced, compared to the American commanders, and more importantly (2) the US forces were far far better armed, supplied, and trained. At best - from a Filipino perspective - the Philippine Army might have won a few more skirmishes, but I can’t see any way it would have won the war against the US forces deployed and in reserve.
The more interesting question, in my mind, is whether Filipino nationalism would have been “healthier” after the war if there had not been the residue of anger by followers of Luna (especially Ilocanos) against Aguinaldo, who was believed to have been responsible for Luna’s death. The long-run implications of Aguinaldo’s role - real or imagined - in the deaths of both Bonifacio and Luna (*) have festered within Filipino nationalism ever since.
(* Originally - four years ago - I wrote “Aguinaldo” instead of “Luna” here. I never noticed it till now, and if anyone else did, they apparently didn’t bother to say so. Corrected, nevertheless.)
