I'm absolutely for a stack size limit, because in any game that doesn't impose some sort of limit the game swings towards putting all eggs in one basket approach, which leads to rather boring game mechanics: build up phase, train phase, stacks of doom clash - one player wins the other player dies. Basically HOMM style of gaming. So very static, not very dynamic kind of play.
So there should be some kind of limit. Preferably a modable limit. I would appreciate some kind of special game mechanic attached to it. But please, please not something like a bunch of techs like Logistics+1, Logistics+2, etc. this is such a bland and boring game design. I already hated such unimaginative tech design in GalCiv2. On top of that: I think there should be never ever a tech that grants you a bonus outright, like +1 logistics, +1 move to all etc. (also very often used in GalCiv2...). Good designed techs introducing new game mechanics. They maximal grant boni via proxies like units, buildings, wonders, what ever. I think it is better to have a tech tree that is lean and slim but with quality techs, than just add some 100+ techs that just add not much to game dynamics. So guys, a bit less of GalCiv2 or Space Empires 5 kind of tech tree, more something of Master of Orion 2 (great tech tree concept).
Now to the game mechanics of how I would tackle the logistics issue. Let's keep it to just one tech. As soon you (re-)discover the technology of "logistics" you are able to commit production of your cities on logistics per turn. The higher the commitment to more free slots you receive. With each slot you received you can expand one army with one additional unit. Those extra slots are not permanent - you have to keep the level of production funneld towards logisctics. If you reduce your commitment so you lose your free slots. Should you raise your production commitment then you raise these slots. Please note that it's really up to the player whether he spends the production of his cities on that or not and that it becomes increasingly harder to get more slots the more you allready received. This adds a wonderful dynamic to the game. You don't just receive some flat bonus by a tech - No! - you constantly have to deceide what has priority: more stuff (buildings, units) or bigger unit stacks? Those hard choices make games intressting.