But you are also limited by your spellcaster level. You're not eligible for fireball until level 5. Before that I should think you want burning hands, etc.
Fair enough. I might want to take
burning hands before I have access to
fireball, although I would still be hard-pressed to take
flaming strike after I already have
fireball. Most of my experience with flexible class (and class-free) systems are also level-less, so that wasn't something I'd taken into consideration. In a game like Shadowrun, for example, all of your spells are available during character creation.
And if you want to do more than throw fireballs, you Have to take something else. But what you take is Your choice. If All you want to do is blast, you should be able to do that; but don't call yourself a healing cleric.
When it comes to game design, one thing that a lot of free-form games fail to consider is that a choice between un-equal options is not a real choice. I'm not going to choose a spell that I'm unlikely to ever use (because I already have something better, for situations where it would apply) over a spell that I might use (because it applies in a situation that I don't have covered yet); and it's kind of a cop out for them to present it as a viable option.
As a more clear example, imagine that a 5E-style warlock was given the choice between Proficiency in a new skill, or +1 to hit with daggers. Even though neither option improves the warlock's core concept, the skill proficiency is something that might actually come up, while there's no reason for the warlock to ever use a dagger (and +1 to hit would not change that). It's not even really a choice.
I'd also think with this flexible spell system, the player should be able to come up with some RP reason for the spells s/he picks. If s/he tells the DM that s/he wants a fire mage, s/he should have to use that as a guide in spell choice.
Players can come up with an RP reason for any choice they make. One very old lesson in RPG Design: don't gate mechanical benefits behind role-playing considerations, unless you're sure that the RP is a sufficient drawback to balance it.
If one player conceives of their character as an impulsive fire mage, while the other conceives of their character as a calm-and-collected Batman-style king-of-all-trades, then the game shouldn't un-duly reward the latter concept over the former. Players shouldn't have the option to play a character that's
just better than another character.