Sub-Par Idea Sets:
Espionage, Naval and Maritime are not good and probably should not be taken by anyone. The reasons are similar, as well -- the mechanics that they support are just not strong.
In EU4 naval combat is just annoying, not useful.
In EU4 the covert activities are a utterly useless compared to the CK3 intrigue system. A high skill ruler in CK3 with the correct intrigue talents can work absolute miracles. In EU4 picking Espionage will make you marginally quicker and more effective at a half-baked set of mechanics.
Because of the bad mechanics that they support, I don't think that you can conceivably buff these ideas enough to make me take them if you stick to the "theme."
Beyond this, I think honestly all of the ideas need a good polish, because many of them improve mechanics that are not as important. For example, in Espionage ideas there is a -0.10 corruption/year. When we had corruption as an "anti-blobbing" mechanic, this was somewhat useful (as was some religious mechanics and estate mechanics). Now that we have governing capacity, that "power" got moved to Admin, which was always going to be picked by a "play wide or play tall and kind of wide" play style, even without the +25% gov capacity.
On the other hand, Innovative Ideas is not useless, just a bit more situational. You could keep this "in theme" and buff it enough for me to consistently, rather than selectively, select.
Religious has its defenders, but it's objectively weaker than it used to be. While Deus Vault is great, and stab cost is nice, almost everything else is relatively easy to work around. While the culture conversion cost is mandatory in a one-culture run, there is really no need to culture convert. While the different religion penalty is bad, there are easy work arounds -- Burgher priv and/or trade companies and/or humanist. If you are going to play a "rare" religion (e.g., Sikh or Orthodox) or you know you are going with Quantity for certain, then Religion is right for you.
Updated Idea Ideas:
Anyway, here is my suggestion for some re-evaluation of idea groups.
First: We should take Espionage and Maritime and break them up. The good things in both can be spread around and put into Aristo and Naval and we can restore some AE impact to Influence. Naval will still be meh, but all the meh will be in one spot at least.
Second: In place of the now vacant diplo-based idea groups, we can put a Civilization-based idea group that is only available if you are in that civilization group -- just like the government based ones in the military super-group (Horde, Divine, Aristo, Indigenous, Plutocratic). We could break it down how you like, but something roughly like a simplified Huntington's "Clash of Civilization" model (the book, not the game) could have: Western, Islamic, Hindi, Eastern, Tribal.
Third: In place of the somewhat under-performing Religious and/or Innovative ideas, I would have a similar choice based on one's religious group. Here, to mix it up, we can have a Monotheism Group (Christian, Islam, Judaism, Sikh, Zoroastrian), a Polytheism (Hindu, Norse, Fetish, Animist, Natives, etc) and an Eastern (Tengri, Confusion, Shinto, Buddhist, etc).