TheNiceOne - That would be awesome if you decided to include an option like this in EE. I have been looking at adding EE to my set of installed mods, and this would certainly give me another reason to do so.
I definitely agree that you would want to keep it as optional, since as you said this is a bit outside the scope of EE. But, if the only options are basically either to re-create what you've already done in EE or include it as an option in EE, I certainly hope you have the time and desire to add it to EE.
The fact that one grand soul gem can be wasted by a petty soul and then not be filled more has bothered me, so a solution to this has been in the back of my mind since I started working on the soulgem repricing option for EE. And I know how to make it work, I just need the time to do it

Question regarding the multiple souls idea you mentioned: if I kept adding lesser souls to a Grand Soul Gem, would your intent be that eventually it would contain a "grand" level soul?
Yes, the idea was that Petty is worh 1, Lesser 2, Common 3, Greater 4 and Grand 5, and that for instance two Petty + one Common would count as 1+1+3 = 5 = a Grand soul. Not completely accurate, and maybe it would make it too easy to get grand souls in grand gems, but would streamline the gameplay.
If so, even if you had a lesser soul in a grand gem, could you then capture a grand soul to "top off" the Grand Soul Gem and thus it would contain a grand level soul? If that is how you envision it, it's an interesting idea that basically does what I'm looking for: provide a means to maximize soul gem usage.
I envisioned that a Grand soulgem with a lesser soul (2 of 5) would only have room for a common (3) soul or less, but if I made it, it would be easy enough to make it an option that the Grand soulgem would be completely filled (with the remainder lost) by a greater or grand soul as well.
I might have a simpler alternative way to do it, it will work no worries, but its different way of doing it and your going to need plenty of cash
TheNiceOne if you are going ahead with a plugin for EE, do keep going with it, dont let me deter you in any way, cause mine is just thinking outside of the box, no tricky stuff and hard to explain without giving it away but yours may be far better then what im doing. Maybe by the weekend i might have it ready and add it in the Oblivion gate spell mod, plus having a couple of blank Staffs that you can enchant to what ever you like
Good luck. Alternatives are always good, and if I add something like the above to EE, it will be completely optional, and therefore something that can be turned off for players prefering your way of doing it.