There are approximately thirty missions which must be played in order. To move from one mission to the next you must achieve the mission objectives. This does have negative repercussions on replayablility, unless you want to try new tactics. The in-mission interface is pretty straightforward. Hot keys allow you to choose which range of weapons you want you 'mechs to fire, whether to run or not, even choosing specific parts on enemy 'mechs to fire at.
Some orders change the cursor when they pass over something that can be used, altered, or destroyed.
You do need to keep an eye on your 'mechs, for once they finish with their current orders, they'll sit there and pathetically attempt to defend themselves if attacked. Especially since moments before the briefing showed you the whole map. Mech Commander also has a huge number of 'mechs and vehicles that you can use. Each 'mechs weapons load out is customizable, giving you the option to completely change the role of a 'mech if need be. Since 'mechs can't pilot themselves, you'll need to keep the mechwarriors that do alive.