Increasing the build time isn't a simple fix-all solution. In the campaign mode, where battles start out with units on the field, the ones with more units get a much larger advantage if the build time is increased - especially if they have more Hunters (or if they have some and you have none).
A debuff to resource gathering has the exact same problem - you get bonus recruits for taking construction points, so the more units you start out with, the bigger your advantage will be.
Decreasing the overall population cap seems like a better idea - the way it is now is too large and encourages longer games.
There's also the problem of the RTS map being able to research anything quickly if you have the base unit, it makes those upgrades from the Campaign map pretty worthless.
That is exacerbated by the inflated population counts, with 7000-8000 Recruits per map, getting all the upgrades is cheap and affordable.
I don't think outright banning research is a good idea either, it means there could be no way to counter. I think the beast way to make research matter is to have counters should come at a hefty cost.
Suggested Improvement: Drastically increase the recruit cost to purchase upgrades in the campaign's RTS mode by something like 5 times, so instead of something costing you only 20 recruits to research, it costs you 100 - a pretty sizable chunk of income. Probably don't increase the research time, just the cost.
That should force you to choose between temporary research and unit production, and it increases the value of upgrades you bought on the campaign map.