Other than your personal opinion about it beeing bad I don´t see nothing wrong with it out of the points you try to make.
Managing resources to keep the staff both payable and effective is an interesting addition to the game and a challenge for all. If you don´t want that challenge, go with minimum salary staff (or actually the ones you can buy for almost free on the market) and don´t bother.
If you want the extra spark from having a 5, 6, 7 trainer, doctor or PR guy, you have to find a way to purchase him at a fair price AND pay his salary. Where´s the bad part?
In addition, skill level tells you what the staff does. Bonus feature is a nice thing to have, and you might explore one thing or another while doing one thing or another with your team. What´s the true downside?
Unless there´s something clear cut better, why change a system which is pretty solid and working?
Zwei Dinge sind unendlich, die Dummheit und das All...