I'll bullet so it's short sweet and simple. More details can be added via comments (and/or edits)
1.) Lack of transition: If you build into, let's say, Nobles. There lacks a decent medium to make a proper step by step transition into another comp. This is something that allows players to work around the RNG based game that exists in DotA Autochess.
2.) Items: There are many routes items can go. They can be nerfed, you can introduce more complex combinations, etc. Items are too strong for their accessibility. Items > Champions, many times. (In addition, if you have 3 items on a lvl 2 units, and you combine it to make it lvl 3 with another unit that also has an item, it's completely random which you get. I had a lvl3 vayne lose it's bloodthirster for a chainvest. This needs something to prioritize one thing over another.)
3.) Late Game levels: Correct me if I'm wrong, but I believe that it costs 70 mana (or w/e) to level from 8-9. Which is a huge jump in cost. I think it would be worthwhile to test and see if it would be better to lower the cost to level late by X amount and get rid of Force of Nature (Spatula + Spatula).
4.) Leona is a complete idiot. ie: Quit ulting dead units, thx
5.) Rerolling: Omg, can I please place a unit out while I reroll. I'll have like 2 units ready for 3 star and I'll be forced to delete one for another important unit, then on the next reroll that final unit i needed came back.
Conclusion.) I love these games, but overall I think the ability to work around the RNG and transition is the most important of these along with items current state. Players lack the ability to adapt around their RNG, so they have no choice but to force (which doesn't work), so items are a huge reliance, far too much if you ask me.
Post your thoughts, what do you agree/disagree with?