But then nobody would buy weapon upgrades for the same reason they don't buy the PPSh, it just makes your troops decent at one range and terrible at the rest.
Combined arms. Seriously though, that's what I'd hope for - upgrades having a sufficient advantage in their good ranges to make them worth getting (almost certainly coupled with a universal cost reduction to make it work), but enough of a weakness to make not putting them on everyone be the desirable outcome. In my mind, much like the Gren-PG combo, it should feel worthwhile for upgraded Guards to have a few Scripts covering their flanks so an enemy vanilla rifle squad won't break even with it if it surprises the Guard up close...compared to now when it's like "Well, my Scripts have AT grenades".
But let's be honest, rebalancing around that would be rather close to making a new game...especially if, as mentioned, upgrade costs go down because of newfound drawbacks to them, 'cause then all the other muni sinks gotta get balanced around how some major muni sinks became not major muni sinks.