The idea sounds incredibly fun and it is, too an extent, there are some flaws that need to be addressed.
Repitious: The enemies don't change, other then elites (which are borderline OP) and at a certain point you only need to let you ships do the work because enemies don't change.
Income: based on the amount of enemies, and elites give the same as normal? that makes upgrading more difficult later on when prices jump.
Once set, can't move: From what I see, once a ship is placed, that's it. It's good that if destroyed they come back next level, but allow us too readjust them.
Elites: Yes they get their own spot on here. good god they feel OP, killing you within a single volley, and as mentioned, they don't give anymore then the regular units? (Hint: focus them down as soon as they appear, leave the grunts to the fleet, so far rocket launcher seems best)
Range: You didn't explain it, but the area of view should be pre set, not how far the cursur is from your character, as your aiming. Most people will hold the trigger which locks the screen and not know why their vision is so limited. On that note, to get max range you have to move the cursor too one of the far corners of the game screen.
This game is fun, and a pretty strong start, if your thinking about building upon this, which I highly suggest, then I would make a few suggestions:
A story (why your fighting) would be nice, as well as your alley ships being able to move around freely like you can. More diversity in enemies other then grunts and elites (ship types as well, admittedly it's aesthetic, but it does make a large difference). The flagship having it's own defensive weapons (seriously, if it's like a troop transport, sure, a flagship without defensive weapons? logic?) and possibly different locations.
Tips: For those playing, advice.
As mentioned to maximise your range you have to put the cursor at the far corner WITHOUT firing your gun, as holding the left mouse button locks the zoom where it is.
Get the rocket launcher for Elites, when they start appearing, they are you primary focus, your fleet can handle the grunts.
Focus mainly on fleet as they are the ones that get the brunt of the force so you can deal with the elites
Elites only show up one at a time, but there is NO delay between them. When one is down, get too the next one ASAP or it will F your shit up.