In games like Warframe just about every color for equipment and your characters can be customized including what they call "Energy Color" (the color of your projectiles, lights that glow, ability colors, and that sort of thing). I never found it as distracting because you typically aren't using color-coded player attacks to identify one another (the Hero having distinctly orange/red attacks, the Phantom having blue attacks, the Etoile having yellow attacks, and the Luster having whatever color style they have from red, green, white, or gray-ish). With only some weapons having the ability to color photons I feel it could be a fun cosmetic change though it really is up to Sega depending on how hardcoded their colors and effects are.
In this same sense, I would personally like if weapons could be colored and customized in a similar way to our costumes and outfits so you can change the color of the trim of certain weapons and the likes. But unfortunately Sega already has reskins of these weapons available in different forms (such as Fluxio and Rinser which are similarly oppositely-colored) or weapon camos that are identical in shape but not in color (Sigma vs. Gram weapons as Sigma is black-and-green but Gram is white-and-blue). I would not mind the Warframe approach of being able to color aspects of the weapon (or entire parts of it) in addition to the particle colors but I do not know of how many people would actually find that problematic as in Warframe I never really saw much of an issue there other than players using black energy colors which obscures certain visible abilities (such as Nekros, the necromancer-esque character, bringing back enemies tainted in black that makes it difficult to distinguish between a revived enemy and an actual enemy. With different energy colors this effect is much more visible and it is easy to tell that's an ally and not an enemy as a result as black looks "almost" invisible). In regards to Phantasy Star Online 2 in its current state we absolutely have nothing that you "must" see on other characters as all status effects have a universal look to them and the only effect you can actually see from other players are their buffs (Fighter's Limit Break/Overload having a flaming effect, the Etoile's Overdrive giving everyone a glittering effect, the Hero's Hero Time granting a flowing energy look, and that sort of thing).