A system could also be that one can't choose which tech he is researching, keeping anyway the tech tree: it would not be anymore the same thing always, but it would be kept logical.
However, it could be problematic with a Civ4 like tech tree: one can go for Future Techs without having discovered Horseback Riding, which would be problematic if you would have only Horses. Indeed.
Eras would be needed again with such a system probably, representing the technology spreading over the civs.
Or maybe there would be a high probability to find Horseback Riding if you have horses.
In the case of Iron / Copper, that appear on the map only with the critic techs, on the model of Civ4, entering a war would influence the research orientation. (tech groups needed)
This way, a pacifist civ, if it is lucky, could enter a war suddenly if it discovers Bronze Working, and the attacked civ, say pacifist also, would have more chances to catch up with its enemy.
Ideally, some would say, one could orient its research intentionnally in order to prepare an invasion; but I don't like this idea, for all the reasons I mentioned: one does not think "let's find a new alliage to kill our enemies right now!"
EDIT: another idea could be that to consider the tech orientation possibility as an effort to steal a technology. It would make sense as Science, in my system, would be the fruit of contacts. Then, if a civ you have contact with have a technology, even if you are at war with it, it would be possible to orient your efforts towards this very tech, and only then. Something like that. However you would have less chance to find a totally new technology that you could possibly trade with your neighbours, being the cost of being just a 'follower' rather than an open minded creative one.