I think people have your proposed class changes covered so I'll just comment on this:
I'll grant you that these are not used very often, but they are used. There is a point early in HW where you'll probably want to use one. Rather than removing them completely, I'd much prefer to see the places they can take you expanded, so they're more useful.
We have this already. There are foods to increase your choco's xp gain, increase healing and increase dps. These can be bought off the MB or grown in any garden if you have access to one. Feeding any of these foods to the choco 10 times in the stable makes it his favourite food and that will increase the benefit when you use the food in the field (choco can only have one favourite).
And we have this too. Max level is actually 20 and you get there by feeding the choco a Thavnairian Onion each time it reaches a new level after level 10. You can get 2 onions via sidequests and you can buy them off the MB or grow them in a garden. Growing is very involved and will take some time, though.
The skill tree is there as well and you should have been choosing skills for your choco already (assuming it isn't still level 1). You can choose to concentrate on healer, dps or tank (choco tanking isn't great though). When your choco reaches level 20 it will have all the skills from all 3 branches. You get a barding set every time you max out a branch so by the end you'll have 3 sets (these are auto unlocks, each set just appears on the barding list).
Mistells are part of MMO life I think, and I've made quite a few blunders in my time. However, if you r.click the person you want to send a tell to so their name appears in the text box and then press enter before writing anything, this will open up a private channel for you where everything you say will automatically go to that person until you select a new channel.
Hope that is helpful and glad you are enjoying the game.