Indy as a trilogy IS hit or miss but Raiders is one of the all time best films in cinema history, and for that alone despite temple of doom I don't think it's fair to put the bourne movies on a pedestal next to jones, trilogy or not.
Same logic for Godfather. I & II as just SO good ameircan classics its unfair to even try to put bourne above it, despite III's weaknesses. Raiders makes up for any failings in the later Jones films out of being basically universallly seen as the greatest action-adventure film of all time. And well Godfather is the fucking Godfather.
I don't care if either had weaker entries than bourne, when godfather/indy are at their best bourne's 3 consistant solid-to great films can't compare.