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No issues playing RA1 here. I didn't have to change or adjust any settings. It plays like it should. I managed to get through the first 2 parts ot the training without dying but died a few times in the 3rd. Then have been doing already in the furthering missions, going through it more quickly than I thought I would have after all these years. Having played it before definitely helps knowing what to do!
I'm not ashamed to admit that I had to play RA 1 on easy. I'm playing with a Logitech gamepad which I feel does a fine job. I also had to lower the frame rate as flying through the ice cave destroying probe droids was just too frustrating. I've finished the game now and am enjoying RA2 without changing anything but the joystick sensitivity in the options menu.

These games sure bring back some great memories. It has been worth it to play them again.
The controls make a lot more sense once you realize for hard turns they want you to also pull up.
I just played through RA1 on both Mega CD and PC; interestingly, the controls on the Mega CD (which had a digital joypad) were considerably better than on PC. Even tried PC with a digital joypad, but no better.

Only disadvantages of the Mega CD version are that the FMV quality is shocking (super low resolution because of the slow CD drive plus aggressively dithered 64 colour output), it's missing a level (albeit the absolutely terrible shoot the probe droids in a network of tunnels one) and there's a tone of slowdown whenever things get busy on the screen (for busy, read more than a couple of tie fighters and lasers).

On the plus side, you can at least get the cursor to cover most of the screen and it's better at telling you where to go in the asteroid field to not get taken out by floating rocks...