I agree with getting rid of technology trees.
To make game interesting I would however introduce more materials like bronze or stone, obsidian in case of making weapon/armour. I would introduce also luxuries for trade, so perhaps you have no iron, but you have something to trade for it, or if you are rich, mercenaries would be an option.
I would love to for a change to play in a game where you made/produce every weapon or armor, then put it on people, who then cannot work for your empire. The size of your army and its character would be bound to what you can make, money you can spent on maintaining your army, and how many people you are willing to spare. So one choice in game would be how you balance your economy/trade according to resource you have got.
Research should be reserved to magic only. However, I would divide it into categories like: runes (weapon/armour improvements), global enchantments, summons, war magic etc. Spells available to research I would also bound to shards you own. Some spells could be researched only if you have enough magic power available, let's say three water shards. The choice would allow you to specialize your strategy, since the power of spells would progress according to the level of research. To make things more interesting, you could link spells with shards directly, if you loose them, you cant cast spells you researched ….
Right now late researchers demand lots of time, yet they bring a little of improvement. If I have a choice between one late game magic tech or 12 civics techs which I so far neglected, 12 civics will always beat it. It is not the case, for instance, with dominions when some late research is so powerful, that it better than 6-7 early researches in other categories.