The spells and skills which remain unknown in the game are higher level ones, not dropped or sold by anything in Cyseal. Nothing we've been told or learned suggests that there are a bunch of low-level skills which no one has found.
Being able to choose a skill selection is not remotely close to "the same as choosing when to level up". Getting the desired spells is not inherently unbalancing. A lot of the time, you CAN get the skills you want to use on your characters. By your logic, that should obviously break the game in half and make it laughably easy. That is not true.
The idea that having a skill selection of your choice makes the combat boring and predictable is provably wrong by actually engaging in combat. Unpredictable things happen all the time. Attacks you counted on hitting miss. Enemies unexpectedly pile attacks and statuses on a character. Status effects disable a character you thought you would have use of. Mis-aimed lightning bolts stun your own characters through invisible pools of blood and water. Party members get killed. If you're not finding the combat challenging enough, what difficulty are you playing on?
