I confess I'm not very familiar with editions of D&D past 1st edition AD&D, so the following may not be the first time this idea has been expressed. (I'm fairly certain it has already been expressed in some capacity, if not an official one, by someone. I'm just recording some thoughts on the subject.)
It seems to me there ought to be more to differentiate clerical spells from magical spells than their source. I addressed the idea of changing the nature of verbal components to reflect the communicative role of clerics (spreading the faith), but I think the nature of spell selection lends itself to modification as well.
If magical spells are selected and memorized as a matter of forethought and strategy (an intellectual exercise), perhaps clerical spells should be chosen only in times of need (an exercise in faith). Unlike magic-users, who owe their powers to academic study, clerics owe their powers to their deity and their faithfulness in serving that deity. (This is not to say that clerics do not engage in study, but that their study is of a theological nature rather than quasi-scientific inquiry.) A cleric should not have to guess which spell may or may not be useful in advancing his or her patron deity's divine plan. Rather, when the time comes for divine intervention through the agency of the cleric, the right spell within the cleric's capacity should be available for casting. In other words, a cleric prays daily for his or her due allotment of spells based on his or her level, not for specific spells. When the time comes to cast a spell, one spell slot of the appropriate spell level is marked as having been used for that day. If the cleric's mission necessitates that three cure light wounds be cast in a single day or one cure light wounds, one protection from evil, and one light, so be it. It is the deity's will. Clerical magic should, after all, be miraculous. It is a little less than miraculous for a cleric to be forced to admit, "Well, remove curse would have been useful, but I'm afraid I picked locate object instead. Sorry." Aside from falling short of inspiring awe, it doesn't even resemble how divine magic is presented in mythology or literature. The cleric's deity should either enable the clergy to predict which spells would be needed (in which case the referee is choosing the spells for the cleric each day), or the cleric should be able to invoke an available divine power when the need arises. The latter more accurately reflects a priest's decision of which prayer to say or which verse to read on a given occasion (and this ties into the idea of reciting an extemporaneous prayer when casting a spell).
Does this unbalance the game? Does this flexibility make clerics too powerful? I haven't playtested this yet, but I think the fact that clerics must act strictly in accordance with their religion or lose their spellcasting ability is a strong limitation. Certain deities may even render the casting of a spell impossible on a case-by-case basis if it is judged to be a frivolous (or maybe selfish) use of divine power. Magic-users, of course, have no such restrictions.