That's not a tradeoff...that's an excuse to get rid of all item creation feats and pick up other ones. Weee, 17th level, and a mere 9th level spell slot subs for EVERY item creation feat, AND gets rid of all the time neccessary to make magic items?
Riiiight.
the 25k Limit is what Frank and K referred to as the 'wish economy', i.e. it's only items above that value that are truly valuable, otherwise, anyone with an efreeti in their back pocket can get something worth less then that.
The xp cost is there so that's not abused.
The 25,000 floater xp to have 5 wishes is not truly neccessary. Basically you just make scrolls of wish to replace the ones that are not in your head. Also, you can explicitly accumulate excess xp and NOT level up, if you so choose...levelling is not something forced on you, it's something you are allowed to do.
As for Miracle...this is the 'hand of god' spell, directly asking your god for help. Wish has no such limitation. Sure, it's fluff...but it's important fluff!
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I like the idea of multiple bonuses, but you have to remember that bonuses are abused by ITEMS, more then by casters. I.e. the 20 ioun stones of Exalted, Sacred, Perfection, Shield, equipment, circumstance, dodge, insight, luck, profane, vile, deflection, armor, natural AC, competence, morale, synergy, power, cover, and Haste bonuses to AC. +1. Each of which can be enchanted up to +5, some cheaper then others.
Stacking like this is very bad news. It's why they got rid of so many bonuses in 4e, and 3.5 really needs to cut back on the possible abuse as well. Best way is simply eliminating bonuses, second is having different ones cancel one another out, and third is having them not stack.
Das Bier!===Aelryinth