One of the things I've grown to like about R-Type Command is that even though it may seem overwhelming and complex in the beginning, it gets even more complex than that. But the game doesn't inundate you with everything you need to know starting in the beginning. Instead, it slowly introduces new things one mission at a time.
For example, a few missions in, I finally had enough supplies to create a support ship that can repair other ships. Unfortunately, I was too attack-happy and used those supplies to get another type of offensive ship. I thought I screwed myself over because in the next mission, more than half my fleet was in desperate need of repairs after about the 3rd phase. I tried to bail out and quit that mission, but that counted as a failure. Luckily, failures still garner you some material to upgrade with.
Unfortunately, I still didn't have enough material to upgrade to a ship that can do repairs so I started the failed mission again, being careful this time instead of plowing my way through unknown territory. What I missed the first time around was that there was a docking bay on the terrain that I can use my existing support ship to capture. Once captured, I can dock any of my ships there for a turn and replenish their health and numbers. That was the key to winning the mission.
Images courtesy of Atlus.