First, I want to confirm that it appears that ELC is involved in this. With ELC enabled, my test wizard with Great Intelligence feats has spells from the slots due to the greater INT cleared. With ELC disabled, the slots are not cleared.
The stat bump approach doesn't work easily for shifters who lose spell slots due to unequiped/re-equiped WIS bonus items (or other spellcasting stat bonus items if the shifter is also an arcane caster). It's an incomplete solution even for that issue, since the PC will have those slots cleared when he unshifts as well, which is pretty much just as bad, since he wasn't doing much casting while shifted anyway. A stat bump that lasts for the whole shift might work. But, without a lot of care, it would end up capping the wisdom of toons who don't wouldn't have otherwise had it capped (potentially a big deal for toons with monk levels or shape abilities whose DC benefits from wisdom). Sadly, Bioware didn't provide an OnUnshift event, so we can't also add the stat bump when the toon is unshifting. And, stat bumps don't address the issue of bonus spell slot items.
Regardless of it's impact on shifting, a stat bump doesn't help much with slots cleared on PC entry for many toons because the temporary stat bump is still subject to the +12 cap. So, PCs with +12 worth of gear (which will be many epic toons, even on mid-magic modules) are already capped (and will see no added bump from the temp stat boost) and will still have the slots from the Great * feats cleared (since those aren't part of the cap).
Part of the problem here is that Bioware didn't give us a bonus spell slot effect. That way, we could give bonus slots as a temp effect while running ELC (or during OnClientLeave or whatever) and the extra slots would hold the spells until the Great * feats were re-applied.
A bonus spell slot effect would also help deal with the shifter issue, since a bonus spell slot effect could start with the polymorph effect and would keep the slots from clearing until the toon unshifted. Unfortunately, that might require a heartbeat script to check when the toon is no longer shifted so that the bonus slots effect could be removed. (Just linking the effects may not work, since bonus slot effect would likely go away before the just-unshifted toon got his gear bonuses re-applied.)
However, as best I can tell, ELC either runs before OnClientEnter or ELC unequips gear. I am guessing the former. I think that foils many approaches.
For instance, I wrote some code for the OnClientEnter script to temporarily add the bonus spell slot item properties to something the toon is wearing (the chest item was default). To be honest, this is the approach I thought would be the easiest to get working (or at least to try). But, no dice. The script runs, but the toon still has spell slots cleared. I don't know much about how the mechanics of ELC work, but it seems to have run before OnClientEnter. If there is a way to apply an item property to a just-logged PC's gear before ELC runs, then I think that would do the trick. I just don't know how, since it seems the OnClientEnter is too late.