Could you upload a downloadable HTML5 version (zip) for play on other OS's? I would also agree that the scroll speed for switching flagging options needs to go way down. I think it would be a cool idea to make more options than what are there maybe a like a stun that prevents the mines in a specific area from activating their abilities, there could be an upgrade that allows for extra uses for the limited abilities (scanner and disarm), maybe a ability that reduces the time for other time based abilities to go down (this would mess with the balance quite a bit though), you could also add "upgrade paths" to each one so they increase in ability strength but I am not sure if this is what you are going for
A smart idea would be adding difficulty settings as well to keep beginners from leaving to quickly. The difficulty kind of spikes at the end two if you don't know how to play well.
Another idea for different game modes is an option for instance endless, timed, base, or modified.
It would also be a good idea to add more structures and mines (if that is even possible), maybe a structure that blocks abilities for a amount of time(probes sent) or it could be a mine