You can see a summary of how your score was calculated at the end of each level. It's made up of 3 things: 1. The amount of money you have left over 2. The resale value of your towers (how much you would get if you sold them) 3. 1000 points for each core left at the end (24 x 1000 = 24000 if you don't lose any cores)
So to get a higher score you should: 1. Spend the least amount of money possible 2. Use the fewest towers possible and, where possible, use towers with the best resale value 3. Be sure not to lose any cores
It's also good to wait as long as you can before you spend money to build or upgrade because it earns interest until you spend it. Also, try to avoid using the laser because you don't collect resources for aliens that you kill with the laser (the one that shoots from the sky, not the laser tower).
For almost all the levels that you can use cannons you can complete the level with gold easy by just using cannons and a couple temporal turrets. Either use as few cannons as possible and upgrade them to red or use extra cannons but leave the green.
The more upgrades you have seems to lower your score too.
cash you have + what your turrets sell for + cores left
having a lot of spare cash at the end increases the score having fewer turrets increases score (you can only sell a turret for less than you bought it for. so you lose cash this way and cash = points) having the largest amount of cash in the bank that you can, gives you the most interest. place your turrets well so you don't have to spend as much money on them.
use the least amount of resources possible to achieve the desired outcome. that leaves cash in the bank that gets interest. ideally the enemies should die right before they leave with a core. if you are killing them early on, your turrets are too powerful. you could still stop them with less resources spent.