If over used, or turned into a conviniant
Dues Ex Machina sure. but it hasn't been. So RD is one of the best fliers ever, so what, she's still an interesting character. How many episodes have been about RD being better then everyone? One, Sonic Rainboom, which even then, yeah she did something every-pony thought was impossible, but it's made clear she was almost paralized with fear before hand, it wasn't a casual, "Oh time to go be the best, so bored"
The others you may mention, nope they were about her WANTING to be the best at something, not her ACTUALLY being the best, which that right there, the fact that she more often wants to be doing better at something then she is, invalidates the whole, "It's boring because she's the best" argument, if she was that good, there'd never be a time when she wanted to be better.
Yeah she's brash, she over confident, but we have seen time and time again that the majority of that is just a mask she uses to hide her deep sense of insecurity, she does NOT, at the core of her being, believe she is as good as she acts like she is. Her constant showboating and glory hogging is as much to try and quite that tiny voice in her head telling her she's not good enough as it is just being a glory hound. Sure she likes the praise and all either way, but it's the fact there is complexity under that facade that makes her still interesting.
And yes lately the writers haven't been doing a really good job of showing that, but it is still there.
Build a fool proof system, and the world will create a better fool.