If they want to make money through their free-to-play game, they should focus their strategy on content that doesn't effect the play of the game. It worked just fine for Path of Exile.
A big flaw in the grand scheme of skill tree pitfalls is player disparity. While tree resets are rationed out once a year or so, the problem persists that any player can be a new player, and the new player will not know better. They will max out HP-Up and T-Def Up, because those are options available to them on a tree that costs points and scales on a curve -- therefore they must be more important than those percents that scale linearly. You get more numbers for fewer points! And now everyone hates you and doesn't want to play with you, but you can't fix your mistakes.
Then mags offer pitfalls through the feeding method constantly patronizing you with a DEX stat going up, but the DEX stat remaining ambiguous. So a novice player will either have a mag with 150 atk and 50 dex (or whatever the ratio ends up being), without being any the wiser because the game doesn't punish this behavior, and subtly encourages it. "Oh I'm out 50 attack, but the tree gives me 50 attack for 10 points, it works out." And now everyone hates you and doesn't want to play with you, but you can't fix your mistakes.
Fixing the problems:
1) Focus the scope of pay to purely cosmetics and storage space. This does not infringe on the gameplay in any way, and players will always want to buy cool costumes. And while this already exists, I'm 110% certain a player would pay more money to guarantee the cosmetics they want, over strictly gambling. And they will still gamble anyway!
2) Remove cosmetics from the player shops, or wall it behind rare trade passes and premium. It's obvious why they don't do this, and it's because of the current gambling aspect of cosmetics as-is, but its a huge hole in their wallet. If you can just run TACOs for a week or two to buy a cosmetic that cost someone else $5, that's $5 Sega isn't making. Times thousands of players. Oops.
3) Add refund points to the skill tree. Either have it cost a large sum of excubes, or a moderate sum of star gems. This would allow players who screwed their tree an immediate way to fix it, at the cost of playing the game to do so. Which means the player plays the game more, and is more likely to buy cosmetics! \wow\**
4) Reduce the cost of, or add alternative ways to fix mags. 50 excubes per point is a lot if your mag is missing 50+ attack points. Excubes that ironically could be used to affix more damage on gear...
5) Fix the god damn skill trees. It's not that hard.
Add more conditional damage values, more niche abilities, more weird and wonderful 'stance' skills. Make the 'raw points' values linear but worth the cost of a skill point.
My favorite skill tree in the game is the Force, because you have to choose what element(s) to specialize in. You cannot master everything. You have to decide what element(s) you like to play, and play your own Force instead of just "a Force".
Every tree in the game should be like this. It should encourage specialization outside of just "pick your class". And in doing so, adding a ludicrous number of things to spend points on, you give players the opportunity to feel like they're their own character and not just defined by class name. "I am a Hunter" is mundane and boring. "I am a Hunter that becomes more powerful when my allies die" is exciting, fun, and causes interaction with the other players you play the game with.