I'm going to start of praising the present idea of how magic works now. I enjoy the system that is in place for how spells work based on what level they are cast at and I feel that this is a great starting point for Pathfinder 2.0. However, I do have a few issues and suggestions for improving this implementation.
Starting with Spontaneous casters such as Bards and Sorcerers, I find the limitation placed on what spells they are able to heighten very restrictive, to the point that I and my groups don't enjoy playing them. Only being able to use Heightened spells learned at a heightened level, replacing options for learning higher level spells, and getting to select 2 (or 4 with a Bard feat) spells known to freely heighten feels punishing.
My solution to this problem is a simple one: get rid of that restriction and let spontaneous casters heighten any and all spells they know.
I understand that this may seem a bit extreme and favoring of the spontaneous casters, but in my own experience it hasn't been at all game breaking. As the casters are still limited by the number of spells they are able to cast per level per day, giving them a bit more versatility in the power they are able to cast their spells at has only improved player experience with the system.
Next, a look at prepared casters such as clerics, druids, and wizards. Given my suggestion, it may look to favor spontaneous casters over prepared casters, and it would if nothing were to change for prepared casters. Given the existing rules for preparing spells and the reduced number of spells per day of all casters (maxing now at 3 per spell level) I have found there to be a distinct lack of interest in these classes (save for the cleric which is seen as "needed"). Having to prepare specific spells to specific spell slots, and choosing to heighten spells when preparing them, is a very restrictive system. I understand this is how vancian casting as always worked, but I feel that this is a great opportunity to change the system to make it more fun and intuitive for players.
For this, I look both to D&D 5th Edition and to your own Arcanist class, in which a character prepares a number of spells per day, in essence creating a spell list which they can then cast from spontaneously. The Arcanist is a great class, and I have found players enjoying them a great deal more than traditional wizards. The system is flexible, but still gives those who take time to research and prepare the right spells a distinct advantage, as has always been one of the strengths of the system.
I even feel there is a great system in place for determining how many spells a prepared caster gets to cast each day: proficiency. In my testing of the system, prepared casters could prepare a number of spells per day equal to their Proficiency with spellcasting + their Primary Attribute modifier (INT for Wizards, WIS for Clerics, etc.) regardless of the spell level, leaving it to the player to determine if they want to prepare more higher or lower level spells as lower level spells provide them more diversity vs higher level spells offering more powerful results. As with spontaneous casters, prepared casters could then heighten their spells as they wished when casting them, selecting whatever spell slot they wished to use.
I've shopped this alternative to both my own players, fellow DMs, and to a Pathfinder FB group to get any feedback on it before posting it here. I hope you find it useful in some way.
Best regards and keep up the great work.