I stumbled upon this game and I was addicted. This is the winning strategy.
If you like Ages of the Empire but have no patient, this is for you. There are sufficient variations to apply your warfare theories but the rules are limited so the game can be defeated with not too much practice and research. So, it won't last forever, and you will be back to your real desktop very soon.
The Pellet tower is like Napoleon's foot soldiers. They can hold their lines well, their fire power is decent, but they fire too slow. You needs lot of them. Although their damage/cost is good, the (rate of damage) / cost is poor compared to the Squirt Tower which fires much more rapidly. They do not worth upgrading for more damages. However, like pawns in chess, they are very important. They are cheap, they are plenty, they are disposable.
The Squirt Tower is like machine guns or cannons. The rate of damage / cost is best as they fire non-stop. This is the main weapon of choice.
The Bash Tower is like a land mine redeployed in a short time after every explosion. Or it's like a fixed cannon. It has the best damage/cost ratio. It fires very slow but it damages enemies all around it. It's complements the Squirt Tower.
The Swarm Tower is like anti-aircraft artillery. It fires 4 missiles at the same time. It's a little slower than the Squirt Tower, which is for air and ground, while the Swarm Tower is for air defense only. I'm sure this is necessary. In the beginning, Pe and Sq are good at defending the first wave. When all the weapons are upgraded, the Sq seems to be increasing effective. There is a strange value for the last upgrade. It is apparent that it's better to build another tower than paying for the final upgrade. Anyway, one tower is about enough to kill off all aircrafts, except for the flying BOSS, which are almost impossible to kill. But I'm getting there.
All other weapons are not worth it. They do not have sufficient damage at the final upgrade. Just the Sq and Ba can get the job done. The dart tower is pretty good at the Groups but redundant when you fire power increases. I still don't find the Ink Tower effective against anything. The Snap Tower is just too weak for the big Bosses.
One useful piece is the Frost Tower, which slows your enemy down.
The Boost Tower is only useful if you have several towers placed around it. It's may be useful in the final stages when you have a lot of money and a lot of weapons. For example, it only make sense if you have three Sw towers put together to use Bo. Otherwise it's better to buy another one.
The basic strategy is to slow your enemy down to absorb fire. It's the classic square formations to defend against cavalry charge. For the desktop, I came up with the DNA2 defense based on this formation of Pe's. Obviously Pe's are used because they are the cheapest. You replace some Pe's with other weapons, and put others around it.
I think it's the cheapest way to get your enemy run the most, taking fire at all sides, it's also the most compact in terms of area.
Of course you don't use only one. The pattern can be repeated indefinitely, can be packed very closely to fit your desktop defense space. You can rotate it, flip it, to form long strands something like DNA spirals. Typically you shape your strands so you have plenty of spaces in the middle of the desktop for deployment additional weapons, typically air defense.
Actually you don't need anything else but Pe's in the DNA2 formation. You don't need rapid fire Sq because 10 Pe's firing at random is as good as a Sq. However, the Spawn are pretty good at spoiling things. Distributed fire by Pe's cannot deal with Spawns effectively. Every time you kill a big Spawn, you get lots of little Spawns. There's no way to really slow them down and you have to kill them several times. So you need concentrated fire power other than plenty of Pe's.
It should be noted that the Spawns can pass through the gaps some of the times when the squares are barely touching. But when they pass through one formation, they will be caught in the next. Just remember to block those vulnerable corners where the Spawns can escape to their home base. Even for this weakness, the DNA2 is still much more effective when the enemies have to pass on all 4 sides of a middle square.
Basically you block your enemies so they only charge through your square formations. Obviously the first middle square should be a Ba. Then you need a Sq concentrated at the first corner of entry. The position is crucial. If you put it on a middle square it performs poorly. It shoots everywhere instead of concentrating on where you need it. It's optional to have a second Sq at the entrance corner of the 2nd DNA formation. Typically Spawns pass through the 1st formation will be killed in the 2nd.
The upgrade strategy:
A few of the DNA formation can kill most enemies, with just a Ba and two Sq's. You want the most concentrated fire power. So you upgrade the Ba and the Sq on the same first DNA formation as soon as you can. The 2nd Sq should be one or two upgrades behind. I think on the final upgrade, the Sq are more effective with rapid fire, but of course the Ba's damage is impressive. If you survive the initial assaults, it doesn't really matter you upgrade the Ba or Sq first, as long as you don't upgrade all two Sq first. Save some money for the Ba.
Also you need to upgrade the Sw's regularly for each air assault. When you reach the final upgrade, you should buy yourself another Sw just short or the final upgrade. But I'm not sure the final upgrade is useful. It looks like it's better to have two instead of going for the final upgrade.
With the simple strategies you can kill most enemies except for two types of Bosses, the Morph Bosses and the Flying Bosses. Some other bosses are pretty hard to kill too. With mobility, you can certainly kill everything on the ground.
You can trap your enemies within your DNA2 formations by blocking and unblocking exits. They just run around absorbing fire. Therefore only one Ba and one Sq or two will be sufficient.
For mobility to work, you need two strands of formation. When you block one all the enemies have to go back for the opening in the 2nd strand. Timing is very important because unblocking becomes increasingly slow. You want to keep all enemies running pass your Ba again and again. You need very long strands, with 6 or more middle squares each. So you have plenty of time to unblock and block your exits.
I can kill everything except for the flying bosses, which you cannot slow down. With 4 final upgraded Sw I manage to kill 2/3 of a flying boss. So I'm close. I'm not sure Sw is the way to go. Super guns in form of Sq are pretty good. The Bo's are pretty effective and money saving when you have a bunch of Sw and Sq trying to shoot down the flying bosses.
I have no idea how the other defenders defend. I looked at the top score once and the winning pattern is rather misleading. The person could be hiding his tracks in the final stage by selling things and buying things not needed.
I'm sure there are totally different strategies. I rather not look at them because it's part of the fun. I prefer my style, more like a warfare strategy game than shoot them down types.