It has been hinted that the level cap would expand beyond 100 by some staff members before (of whom I won't cite). However, this was in the distant past, and the plan was never set in stone, so perhaps the majority is not devising any post-100 level cap at this present time.
The only purpose I could theorize for any post-100 level cap is for scaling purposes; those who have completed 2 preceding regions have already encountered NPC Pokemon leveled in the 80s, and thus there isn't a broad level cap between their 16th gym opponent and all of the Hoenn gyms a progressively harder challenge. It would diminish the post-Kanto/Johto gym challenges throughout the course of Hoenn if players typically have level 80/90+ Pokemon in their possession, matched up against level 100 Pokemon at best. Due to the rigorous experience system, I still wouldn't concede to that logic unless some tweaks were made to the formula (or at least the "experience gained" formula, so wild Pokemon yield more experience to commensurate better for your exp requirements).
Even so, a better route of action is for players to forcefully deposit all of their Pokemon when they travel to Hoenn for example, and start afresh and select a new starter Pokemon, and the leveling scale would start from scratch again. They would not have the option to withdraw Pokemon obtained from previous regions they ventured in as long as they are on Hoenn grounds. Some tweaks would have to be made to the PC storage system of course (as it's mechanically considered an extension of your party at this point, not allowing you to "deposit/withdraw" but "swap" Pokemon instead), and some may disagree with this - just voicing my theories for any possible reason for a post-100+ level cap, and why even that shouldn't be necessitated as well.