See, the problem with option B is that they'd have to create all new code in order to turn 3 cards into 1 random super card that won't be meaningful by the end of Act II anyways. Adding research points achieves two key goals:
1) It is a very simple solution and, therefore, easy for Larian Studios to implement. You can't expect them to make dramatic changes to a relatively minor problem.
2) It gives the Wizard's Tower a use even after all Dragon skills are purchased. Given that all buildings scale up in price as you acquire more, the lower marginal cost of getting an extra research point from a tower instead of an academy should outweigh the benefit of the academy's slightly more useful cards.
I'd also think it'd be good if Wizard Towers contributed to the Dragon's HP, but I'm not sure how easy that would be to code and I feel that simplicity is critical here.
