Love the mutually exclusive specializations!
Quoting Casorian Emperor,
Hate the mutually exclusive specializations!
There is certainly no right answer here. Being mutually exclusive means that there are effectively less techs to research, and less options to the player (since picking 1 pulls 2 other potential techs out of his list for next time).
On the other hand it provides 3 big benefits:
1. It makes the selection of which branch you are taking much more important. We like decisions that players stress over, you want A and you want B, which will you pick?
When I read about the game, I decided to buy it because you can choose whatever you like to choose. I'm not buying a game so I can stress over things. I can't make mods (well, I probably can but I simply do not have time time, really not), so I'm looking for a mod before I play with this stupid lock-out system, or I'm looking for a refund. The system is also very hypocritical. You can choose a government tortures people into submission but at the same time is a beacon of light and justice, by the clever use of the ideology system, but you're not allowed to develop more powerful production centres that are also cheaper to maintain? That's a complete joke.
2. It improves replayability. You may play the Terran every time, but different specialization picks can dramatically impact the way that game goes, and your abilities.
No, it adds nothing but annoyance about the same choice a second time you play it.
3. It allows us to make the picks bigger. We can do things like provide government type specializations that provide varied and powerful bonuses with the understanding that the player can only have one. Design your own government by the tech specializations you pick as you go up that tree, and design a new one next time.
With a large tech tree, the picks are already pretty big. No matter how much research you do, your civilization is going to slowly advance on all fields or become an expert in one and lack severely in the others. That's more than enough.
As I mentioned there is no right answer, but that was out thinking.
SO MAKE IT AN OPTION. My personal favourite would be to increase the research cost of specialization upgrades. If you go for beam weapons with less mass, then the more powerful beam weapon development will take twice as long. Do that too, and the cheaper beam weapons will be take 4 times as long to research. If it's easy to have a system where specializations are all available and a system where they're exclusive, it should be very easy to make a system where you can choose between the two, or have a third option.
On that trading tech idea: it's again reducing the options the player has. Want two things? Sucks to be you, you can only have one, and you're going to have to hope some other civilization has it so you can trade. Are you a player with a more isolated ideal? Too bad we're not allowing you to do that.