A couple of thoughts on mana:
1. Mana nodes could be improved; additional time (or resources) would yield either extra mana or additional types. Perhaps a scaling system would apply, or say that Fire nodes can also generate Sun or Chaos, but only after you upgrade it to two fire mana. Sun nodes could make Fire and Law; Law nodes could make Sun and Life, and so on.
2. I feel nodes should be more expensive. My first thought would be to make them require a unit to be sacrificed to build and to upgrade.
3. Add an additional resource; call them 'potential nodes' for now. Scatter them much more liberally then "blank" mana is now. These spots can be "worked" into nodes by adepts, but doing so removes some or all of the potential nodes in nearby plots. This would allow for far more mana if you choose to farm for it, but at the expense of a large part of your civilizations acreage that could be populated with cities and improvements.
4. Make placement matter, Nature nodes can only come from forests, Fire from deserts, Water from irrigated plots. This will have a significant affect on Arc & Litch heavy strategies and makes mana type from each palace more important. Then mages from the frozen north can't throw fireballs; mages from the desert can't call forth springs. Trading mana would become more useful and important as well.
5. Make nodes harder to pillage, some barbarian with a wooden spear shouldn't be able to destroy five years worth of mages weaving enchants to make a node. Requiring an adept or mage to cast a spell makes more sense to me, and several might be appropriate, scorch would trash a Water node, loyalty would destroy Chaos, that sort of thing. Alternately adding an action button, (similar to the build icons for nodes and worker improvements) that allows arcane units to pillage enemy nodes would do.
A couple of thoughts on the towers:
1. I can't recall if the towers are national wonders, if not it seems they should be. Doing so would require a minimum of three cities to complete the ToM victory, and having to hold all three cities could be hard enough, rather than trying to defend every node.
2. Allow the towers to be built with at least two of the required mana types with more making it easier, or even increasing the towers specific bonus similar to the way affinity builds up.
3.a. Allow for a production rushing mechanism other than GE's on the ToM itself. I feel that a way to rush rituals would be handy too, similar to sending prophets to another city to boost a foundling culture, or Warriors of Kilmorph to build anything quickly in a tiny town (much cheaper than rushing with gold sometimes). If you keep a fresh stream of mages ready to sacrifice them selves to the cause, things get done quicker. So then you make building the ToM act like building a ritual.
3.b. Alternately make building the towers more like building the spaceship. Make one tower (SS Part) for each mana type and completing the ToM (like launching a space craft) can be done with, lets say half of the towers, but it might fail destroying towers. All of the towers guarantees victory, but it is announced that you've begun and a victory count down timer starts while you wait to see if you succeed. Presumably in this time everyone is likely warring with you before you can declare victory.
Any of that seem workable?