Up to you of course, but I don't understand how making the portal spawn "only" three tougher-than-vanilla Elementals at time instead of your present solution is going to deviate from Bioware's original approach?
Technically, the portals don't actually spawn anything, they are just pretty static animations. The re-spawning process is handled by the AI script of the elementals in question (DWAIR.BCS, DWEARTH.BCS and DWFIRE.BCS). In the original game, whenever an elemental dies, the script spawns another one of its kind near the portal's location. aTweaks currently patches the respective scripts to make three elementals (one Greater and two regular) spawn at that point by reusing Bioware's technical approach which is very simple and clean.
Now, in order to limit the spawns to three elementals at any given time, the entire procedure would have to be handled by the area script (AR2100.BCS) which would require a completely different implementation. All elementals would have to get unique CREs in order to track their death variable(s) and the script blocks which handle the spawn count would have to be rebuilt from scratch. In short, it would involve a non-trivial amount of coding and testing to get this done.
Furthermore, I actually prefer the current approach as I feel that it brings a hint of danger into the portal encounters. For example, if the player isn't careful and always kills the Greater Elemental first, he may eventually get swarmed by a bunch of regular elementals. I find this fitting for an optional quest involving portals which lead directly to the Elemental Planes.