Makes sense actually. However, either Team only has use for one Regi.
Regirock helps Team Magma. It makes a bunch of rocks come together and create new lands above the sea, and/or bury the sea below them.
Regice helps Team Aqua. It creates a bunch of icebergs and glaciers, which then melt due to Hoenn's high temperature. This creates a lot of water.
The player can then go for Registeel to stop both Teams. As a Steel Type, Registeel is strong against both Regirock and Regice, and resists their attacks as well.
It could actually be a pretty decent plot overall. Unfortunately, it doesn't really fits well with the way Emerald lays out the plot, as Team Magma never steals the submarine. It could work if both Team Aqua and Team Magma team up to take revenge on you or something, which usually seems to be the case in most comeback plots.
I say it's not a bad idea...