1: The Magic / Psionics interaction needs to be nailed down.

There's nothing wrong with psionics being a flavor of magic:

As described in SCAG, the average dweller in the Realms would lump 'Mindmages' in with Sorcerers, Warlocks, and Wizards as practicioners of "the Art" and not worry about the details overmuch.

But we run into a problem: Responding to it. Right now, Counterspell doesn't work on psionics, but Antimagic field does. Dispel magic targets one "creature, object, or magical effect", so it feels like it should work on psionics, since psionics is a magical effect. But also says it effects spells on the target, so it really doesn't. This is reinforced by the Sage Advice article (March 2016 if you want to look it up) which refers us to Lesser restoration, Greater restoration, and Remove curse for ending non-spell magical effects. However, these three spells are irrelevant to most psionic effects. This leaves us with three feasible options.

The first is to fully integrate psionics into the current magical system. Talents are treated as Cantrips, and Disciplines are treated as spells of 1st to 5th level, depending on how many points (2, 3, 5, 6, & 7 respectively) are spent to activate the power. By doing so Arcane, Divine, and Nature spellcasters (and their players!) can intuitively respond to psionic usage when encountered, and it adds an in-universe reason why Mystics are a rare breed, since it would allow other spellcasters to counter / dispel them with their 7^th level slots, and still have 8^th and 9th level slots available, an advantage that 15th+ level Mystics would lack. It's the easiest solution, but it puts a burden on Mystic play.

The second is to reinforce the concept "Psionic disciplines are magical and function similarly to spells." with examples. A Mystic is using Mastery of Air: Wind Form? Treat it as Fly, and now you know how to counter or dispel it. He's using "Mastery of Air: Animate Air? Treat it as *Conjure Air Elemental. In a nutshell, if a power in a Discipline does the same thing as a spell, treat it as a spell. Otherwise, it's a non-spell magical effect. This may be the "holistic" solution, but the amount of verbiage it would take to list all the examples is pretty daunting, so either the system would have to be rebuilt to show that when a Mystic uses Mastery of Air: Wind Stream, he is creating a non-spell magical effect, but when he uses Wind Form, he's casting Fly, or else it should be stated as "Psionic disciplines are magical and function similarly to spells, and are treated *as** spells if they duplicate a spell's results, at the DM's discretion." and just left for each campaign to figure out.

The third is a little bit of added verbiage specifying which spells (like Antimagic Field) work against psionics, and which (like Counterspell & Dispel Magic) don't, and why. This appears to line up with how WotC intends psionics to work in 5th edition, and the addition of a paragraph or two elaborating on it would solve a lot of arguments. However, it makes Mystics dangerous, as their flavor of magic becomes something other magic-users can't really interact with. This, too, may be what WotC intends, and explains their relative rarity, as it's easy to understand why a guild of wizards or a dominant religion would take action to discourage psionic learning, and to stamp out Orders in their area when they are discovered.