For me, harder does mean better. I've been playing Pokemon since before I could read, although I stopped for a while until I picked up Insurgence a while back. When USUM released , I got UM, but it was so easy it was boring. Rejuvenation does it right giving the player choice of difficulty modes. I pick Intense, whereas other players pick easier modes, and that's perfectly fine.
One of the main reasons I play these games is to test my mind against challenges others have designed. The other is the story: I appreciate how dark the tone is for Rebo/Reju. It makes the game feel more like an old FF game in tone than a Pokemon game, but I prefer a gritty fictional world to a fluffy, idealistic one anyway.
In terms of design for Mega Stones, I want the opponents to have access to them, but I also want the player to be able to use them if they choose. More Mega Stones for weaker, less-flashy Pokemon is ideal, especially considering that some people might have unusual favorites. Mine is Mawile, and I was overjoyed to see that it had received a fantastic Mega Evolution in XY. What if someone does in fact want a Mega Spinda, Mega Butterfree, or Mega Corsola? By adding Mega Evolution early game and balancing the Mega Stones received early game around the current opponents, it may be possible to find a way to make Mega Evolution as omnipresent as Field effects. I picked Druddigon because it's easy to control the moveset and have it make sense if it's fought around level 20. It's not going to be able to do more than Scratch the average Fairy, and the Mega form will still be slow as dirt. Poison or burn it and it's not likely to give the player too much trouble from then on, or switch between a Fairy and a Ghost until it gets even harder for it to attack effectively due to PP loss.
Of course, I just really love Mega Evolution and want to make it work. It's just such an awesome feeling to watch one of my favorites jump up in power or even to see the opponent Mega theirs and just feel the rush of "how do I deal with this thing" come on.
I agree with your points about explanation of Field Effects, and I realize you're right saying that it would be better to give a brief demonstration rather than walls of text. When I started Rejuvenation, I was blindsided by the different effects more than once until I started reading the attached manual. I didn't think they'd be important, but now I constantly need to keep those issues in mind. I agree that more trainers should also take advantage of terrain/weather: I was playing Reborn today and ran into the Hiker with the level 1 Aron, and I was happy to see that at least one NPC was designed with the weather in mind. It doesn't have to be that extreme, as I'd enjoy seeing even NPCs with, say a Lotad and a Pichu in rainy/water surface area (Ex. a Youngster standing in a puddle who mentions something about him having a "field advantage") in the first area. Those Pokemon shouldn't be any threat even at the early game, but might hit a bit harder or survive for longer in the right conditions.