I definitely agree; tedium is something I'd like to avoid. Now as to the comment about evasion/flinching/etc, it sounds like you've had some bad luck. However, I haven't adjusted the 'hax' values for the game at all from the canon, so if there does seem to be more of that, it's purely your own luck- OR it could be that there are more luck-based elements in play than in most canon games.
By that I mean- does there happen to be an abundance of NPC trainers with double team? I myself can only think of a few, but I don't choose the movesets for the casual trainers (although I could, I've opted to give them their level-up movesets for the time being because anything I choose will probably be better-equipped to handle player teams). So I suppose its possible that the there is an overflow of Pokemon I've assigned to trainers that just happen to learn double team, sand attack, or whatever.
If that's popularly annoying, it can be changed, but it's not something I've noticed.
Regarding Leech seed/paralysis- I feel like you might be referring to those couple Cherubi at the beginning of the game? I don't recall if they have paralysis, but I'm struggling to think of anything else outside of story battles that uses it. Please correct me. Anyway, it's a stall strategy- which is something that's perfectly competitively viable, and takes different tactics to get around than just hyperoffensing your way through every match. I'm not going to say that it's deliberate that I've made it this way with random trainers, but I'm not uncomfortable with it. I'm also unsure why it's lumped into the hax category.
Similarly, I'm confused as to why multi-hit moves are in there. With the exception of Noel's Cinccino (which is, I believe, the only thing in the game that's holding a King's Rock), I can't think of why that would be particularly tedious (except for the time it takes for those moves to finish their animation cycles, something I wish they would change in the canon).
So that leaves us with the conflict you begin with- difficult to level things up without healing which is either expensive or a bit annoying, and you're forced to level other things up because of the level cap.
Let's talk about the money thing, first. One thing I notice in Pokemon games that don't have ridiculously expensive clothes shops is that money is not even an object. Just from battling the 9385 trainers in each game you get to be infinitely rich so that you don't ever have to even think about the price of anything at all. From a gameplay perspective, this is off-putting to me. I feel like there's some decision making lost in not really having to consider the prices of things. Although I understand that at some point of the game it will become futile to try to inspire this thinking, I want players to, as much as possible, have to make reasoned decisions about what they do with their money, rather than just "lol i have 999,948,28apple,492,700 pokedollars; lets. go. SHOPPING~~~~~~"
However, I agree that having to backtrack so often is rather tedious. It's for this reason that I began adding in the Light Shards- and tell me, tyeltr- have you been playing Episode 9 or the 9.5 release? If the former, you won't know about the Light Shards, which are basically one-time healing points scattered about the world for the purpose of making it so you don't have to go back. Although it will not entirely solve the problem of having to heal 'younger' things, I think it will especially help traversing dungeons and areas with them.
Checking out that trope I actually am struggling to see Fake Difficulty in Reborn- however, the article links to "The computer is a cheating bastard" is what's going on. The programmer of the Essentials platform (which I make the game based off of) and I had a chat once about the AI and he told me it does this at higher levels- it basically checks what the player is going to do and THEN makes its move. Its supposed to simulate prediction, but I rather dislike it. In the end, he would not be convinced to change it (it would be a lot of work to do so, so I can't really blame him). In that regard, I am also very often disappointed by the AI and the methods it uses. If I ever get sufficient scripting help, I would like to revamp it, but that will take a backseat to things like finishing move and ability effects, getting 6th gen and Mega Evos in, and whatnot. In short although I would like it to happen, it will likely not in the foreseeable future.