Yes, I agree that if you focus on a particular avenue of strategy (and im not talking about "we build only the best" kind of strategy, but a specific decision to focus economy/tactics upon a certain terrain or behaviour) then you should get rewarded for speicalizing, instead of penalized for not considering a more broad focus.
For instance, you can gain acess to extra specials if you focus on a certain avenue (mountaineering, Desert Warfare, Ski-Troops, Jungle Medicines, Horsebackriding) although you cannot simply gain different specials for switching emphasis throughout the game.
Your entire empire really needs to center around a certain way of life to get access to any of the good specials (or simply any specials at all) ...
This is why I think starting location should have alot of influencing power. You get a basic tech, like Bare-back riding, Mountaneering, Jungle Lore, Winterborne, Desert Nomad ... or some such ... a basic starting tech that you can only get by starting near the relevant resource or in the relavant terrain, and the more extreme your starting position the better your chances of getting the techs. Meanwhile, others without said essential tech can try to delve laterally into the "specialty" tech-tree in order to get a select few, limited techs to try and combat your specialty, but they will be looking at at least 3x the expense (if at all, for instance it might switch to that after a few defeats by your desert bandits, or they might organically switch to some "other" counter if it even exists, say vs horses, although desert is a hard thing to combat against)
Meanwhile, you have a whole tree of specials and randoms, which may or may not be in that particular game, and then you deal with the cards you are dealt with within your specialty.
Upon researching such a key "situational" tech, it opens up its own slot in the tech interface ... its own section, at least if its terrain based. If its simply better archers or horses, it will simply make those techs more likely to appear. Its key though that the player at no time knows the name of the tech they are researching (until the end when they get a title and a description below - perhaps vaguely telling what this could lead to potentially) and also that the User not simply "train three at once" but assign various percentages to each of the 5 or so "specialty" classes. I would say 5 basic, and then a 6th open slot in-case you gain a Terrain Specialty, or some other Key Situational Tech (perhaps based upon Starting Location).
At first you have to divide from a total of 100%, but perhaps with innovations in Education, instead of the old system, you will get more % points to distribute along the tech tree. I don't think Education should be infinite though ... I think maybe 100%->110%->125%->145%->170%->200% ... and for 200% to be the maximum for distribution. Also, you can invest no more than 100% in a single specialty, OR any % points past 100 are used up at only 50% efficiency ... so if you maxed out your education, and spend 200 points on military, it will only be 150 points per turn.
And these % points are all percentages of your total research value. So one faction could be specializing in Acadamies and Schools (Education) in order to maximize the percentage of research (to get "double" efficiency), and others could invest in Labratories, Experimentation, Field Expeditions, Research (like the rainforest bonus) ... to boost raw research capabilities. Of course most nations will probably want to increase their percentage AND their raw research mining, although I would like to see research separate from Economy, unlike Civ 4 ... so that you can have a booming economy, able to by SOOO much equipment ... and yet you did not try to boost percentage usage (teaching the young), or boost raw research mining (enable the Intellectuals to experiment with Nature ... and possibly unsuspecting Citizenns, or rare tropical medicines) ... then you will not gain new technologies at much speed, but you can pay off bandits, Mercenaries ... and Great Works to help your building projects and recruitment projects, or what-not (but they will most likely be "inferior" troops)