One area where 1.1 falls short is in differentiating factions, whether they be pre-made or custom. If each faction had a unique tech specialization/sequence, or you had the chance to choose one during faction creation, I think it would help to differentiate factions much more throughout the game.
For instance, one specialized tech sequence could be Ambush or Troop Concealment. After researching a certain tech in Warfare, a faction that has Ambush as their specialized tech could research Troop Concealment, giving each of their armies a 20% chance of concealment from the enemy each turn if stationary, 10% if moving. Perhaps this is correlated with army size, so maybe 30% - 1% per soldier. Then the person can research Ambush, which gives a 10% attack bonus to troops that were successfully concealed from the enemy that turn. Future techs could increase the likelihood of concealment, minimize the impact of soldier numbers, increase ambush bonus, etc. BUT this tech sequence would only be available to factions that select in faction creation.
Another possible tech sequence could be Shard Enhancement or some such. That faction could research to Shard Domination to gain an extra mana per turn from each shard, Shard Augmentation to increase the effectiveness of appropriate spells by 5% per shard (damage, duration, etc), regardless of spell formula, etc.
Perhaps a Tourism tech sequence, where a faction can research ways to make Gildar off of Arcane Towers, Shards, Lost Libraries, and off of faction and world wonders.
An exploitation tech sequence, allowing greater gains from resources, like clay pits, fertile land, gold mines, etc, but at the cost of prestige and diplomatic capital.
A sword-based tech sequence that gives additional speed, damage and defense bonuses to sword-wielders
The possibilities are pretty limitless. The idea, though, is that the core techs would be the same for all Kingdoms and for all Empires, but each would have this ability to specialize in a particular area, and that specialization would grow throughout the game, unlike the current bonuses which typically stay the same or diminish in importance as the game goes on.