So you mean that if i die at wave 20 and die i still earn some kind of thing which boosts my towers (or whatever) when i restart? That's a great idea.
I meant in a way similar to Diablo III Paragon levels or Hero of the Storm account level. Based on what you do, you get experience to your account which raises your account level after enough is obtained. The amount needed per account level is substantial, so it might take hours of play per level with high levels taking more per level.
Such account levels are quite a trend in gaming recently. StarCraft II Heart of the Storm, Heroes of the Storm, Diablo III, etc all use the idea and it certainly has received positive feedback.
What levels do is something that probably needs to be tried and tested. They could allow you to skip early waves and give you starting resources/workers so you immediately start later. They could increase your unit's stats, substantially and difficulties could be added with harder waves (and more exp, for those that are higher level) etc. You could use the Xenoblade approach to levels (bonus damage vs lower level monsters, reduced damage against higher level monster) to emphasize level differences rather than pure statistics. Levels could unlock additional content (better towers) which could make things easier and are required for harder waves.
I am trying to figure out how to make the towers more dynamic. One idea i had is to make boss monsters drop random items which could be "socketed" in towers, like YouTD does. Even better would be some kind of simple block programming for towers where you place different programming blocks that defines how the tower behaves. If you ever played Secret(Legend?) of Mana there is a feature that allows you to program a robot companion like this.*
There are many ways this could be done.
It could be something simple like "sockets" from Diablo III where you get gems you can insert in them to give an effect. Tower types could have a separate selection of gems from individual towers allowing one to customize their towers before joining a session as well as further customize individual towers. To prevent min-maxing there could be gem type restriction on slots (so no throwing in damage increasing gems in all slots). Effects from tower type gems could be more gem tower gem slots, cheaper tower build costs, easier tower levelling, more tower damage, bonuses for tower placement etc. Specific tower gems could be damage, attack speed, debuffs, area of effect, bonuses against specific targets etc. The gems themselves are dropped from bosses and can be re-used. Discarding weak gems could give an experience bonus. Higher difficulty/level bosses could drop better gems. Possible option for trade and micro-transactions however it might suffer controversy like the Diablo III auction house.
Tower levels could give points on some form of grid (Final Fantasy 12 style) which can be used to unlock enhancements. The grids could be applied at multiple levels (account, per race, power tower type, per tower etc) depending on how much choice one wants to provide the user. These grids can be balanced so that powerful effects useful for high difficulty levels are harder to access and require compromises compared with weaker tiles. Could possibly replace levels even (Final Fantasy 10 style). Unlocking tiles is a possible area for micro-transactions but will cause "pay-to-win" controversy from people.
Some form of talent system could be used similar to that of Xenoblades which allows you to unlock talent branches with points (gained from playing in some way). Each branch has a focus effect (when choosen, here is some customizability) and unlocks talents which are always active independent of branch. Then using a separate point measure (possible from account level?) you can link talents from different talent sources (eg arrow towers linking a talent from a debuff tower) which adds considerable customization options. Costs can be balanced based on talent strength while focuses can be balanced based on each other.
There is the Diablo III approach of levels where levels unlock more customization choices. You could force the player to pick some number of customizations for some element (race, tower type, individual tower etc) from a selection which grows based on level (account or just that element). To prevent min-maxing selections could be forced to certain types of customization (no all damage customizations).
In any case no mater what customization scheme you choose it is important to try and limit min-maxing and other approaches which can break balance. If people can throw enough damage onto something that it kills everything effortlessly then chances are they will never use anything else than damage. Even if an idea for balance seems concrete on paper, in the field it often turns out not viable or anywhere near as good as dumping into something like all damage. If you do manage to balance it you may find that dumping all into a single customization area still is more effective than a variety of customizations in different areas. Hence why many of the suggestions I have provided have methods to force choices in different areas so as to stop people from dumping all customization into a single area and generally make customization balance easier.
There are other geometric patterns than a grid. There could be various modes such as hexagons, maybe some more complicated patterns etc. This could present the player with different challenges and again improve replayability.