The issue is that once an upgrade has been chosen for an ability, it is no longer possible to use the original, non-upgraded form, in most cases.
I would like the ability to still use the non-upgraded form.
If I'm not mistaken, there is already a precedent for this, as Lay on Hands is still cast-able even when its upgrades have been unlocked.
I've found a few use-cases:
1) Same-name buffs don't stack (but upgraded/unupgraded ones do). This prevents multiple characters in a party that share a class from properly debuffing a target together if they have both upgraded in the same manner. For example, if 2 hunters each have Accurate Wounding shot and are attacking the same target, having the option to use the unupgraded version would let each of them apply the debuff, but when on different targets, they could still use the upgraded form to apply the DoT and still enjoy the accuracy bonus from the upgrade. This also applies for multiple users of Hunter's Mark, Sworn Enemy, or any DoT ability.
2) Differing resource costs. For example, say your chanter wants to summon wurms and you're 1 phrase short and have upgraded. Being able to use the original form would let you summon without waiting.
3) The ability picks up a new damage type. Brand Enemy and the healing/burning invocation becomes undesireable when you suddenly come up against an enemy that heals when taking fire damage (looking at you Dorudugan). Did my paladin just forget how to use the basic Sworn Enemy? I'd like to still have the damage bonus, but without healing him in the process.
I assume the original forms are removed after upgrades to clean up options for players under the assumption that there would be no reason to ever use the unupgraded version, but there are a few, and maybe even some I did not think of.