Oh, now that's an interesting idea. Very different from the current system, but I wonder if the two could be pasted together...
How about this: leave the current system in place, exactly as it is. This represents focused, funded, state-mandated research. Additionally, each nation has an invisible "random breakthrough" pool. Several sources can add to this pool (more on that later). Each turn, there is a chance of a random breakthrough equal to:
pool / X + GameTurn*Y + pool
...where X and Y are moddable and will depend on both how we want to scale the pool units and how frequently we want random breakthroughs to occur. They might also be adjusted by certain traits. There's never a 100% chance, and the chance decreases over time. For now, let's assume X = 10 and Y = 1. When a breakthrough occurs, the pool is reset to zero.
Things that add to this pool could include: 1 point per Champion (including the Sovereign); the level of each of your cities; 1 point per 10 levels of non-Champion troops (can troops level up yet?); 1 point per domestic trade route; 2 points per foreign trade route; etc.
Now, when a breakthrough does occur, it's random but weighted. There's no choice involved (you get what you get) and it does not increase your relevant tech level (i.e., no effect on normal research times). As a baseline, each tech for which you meet the prerequisites has a chance of appearing relative to the inverse of its rarity. The sources of pool influence are also checked, kind of like the great people generation mechanic in Civ4: champions make Adventuring more likely, cities encourage Civilization breakthroughs, common troops yield Warfare, trade routes produce Diplomacy, and I'm sure we'll think of something that contributes to Magic. Technologies that other nations already have are more likely to appear.
Thoughts?