I strongly agree runes need to be unlocks. Unlocks are always better. No exceptions.

But I think you need to use more existing systems and mechanics rather than discarding them.

For example, there could be a way to craft "Ascended upgrades".

These would be upgrade unlocks that although 'ascended, do not have more extra stats, instead, they are unlocks. Once unlocked, they allow to apply to that upgrade to any compatible gear, and the stats would depend on the item level, counting as the masterwork version up to level 39, rare up to 60, and exotic for the rest.

To craft them, you first need a 'Blank Ascended Sigil/Rune" that is crafted in the mystic forge with ascended materials (e.g. lesser and normal vision crystal) and materials obtained from salvaging upgrades of all 3 qualities, to get materials from them. For the sake of example let's call them "Ferrite" , "Mithrite" and "Orichite". Normal vision crystals could create runes, and lesser vision crystals could create sigils.

Once you have a blank ascended upgrade, you can craft the ascended upgrade in the mystic forge with one Blank plus a sufficient stack of each quality available of that upgrade, or wildcard materials when the upgrade is not available in all 3 qualities.

So, for example, to get an Ascended Sigil of Force, you'll need to salvage masterwork, rare and superior upgrades of any kind, then throw a stack of let's say 250 ferrite, 75 mithrite and 25 orichite a lesser vision crystal to the mystic forge to the a Blank Ascended Sigil. Then Throw the Blank Ascende upgrade plus something like 120 Masterwork Sigils of Force, 60 Rare Sigils of Force and 12 Superior Sigils of Force to get the Ascended Sigil of Force.

All this would work better if the Mystic forge got a recipe list.

Once you have your ascended upgrade unlocker, you use it and the upgrade becomes unlocked for the entire account. Now you can go to the the build panel, click in the 'Upgrades' section, select a piece of equipment for which you have upgrades unlocked, and you can use any upgrade upgrade unlocked to upgrade your gear. You will also still be able to upgrade using non-unlocked upgrades by getting the item and double clicking them just like now, and if you have them in the inventory they would appear at the top of that panel like how other items like skins, minis and glider unlockers appear now at the top before the unlocked ones.

Instead using transmutation charges, this system will use Spirit Shards as currency in PvE and WvW, since lots of people has tons of those are they are not hard to come by, but are not too trivial to get either. In PvP, this system would be free just like how upgrades are right now, and an alternative to the PvP build panel like other panels in the Hero panel, and will only affect the PvP build, and show all upgrades you have unlocked in PvP. People would still have to go to the PvP panel to unlock the ones they don't have unlocked, though.

Legendary weapons would gain the additional advantage of having all upgrades available in the panel when selected, regardless of your account's unlocks. They would still need to pay Spirit Shards to swap, though.

TL:DR;

• Salvage exiting runes.
• Use materials from all 3 rarities + other materials to get blank.
• Use blank + stacks of the upgrade to get upgrade unlocker.
• Unlock upgrade, apply it indefinitely for a reasonable fee.

This way:

• All those worthless upgrades filling the trading post get used in troves, thus stopping being worthless and getting their prices increased.
• The most expensive upgrades get slightly reduced in cost since less players would get them over and over for alts, thus making them more available to more players, which means that wherever you go it'll be less likely to get people around with bad upgrades in their gear. The better other players get, the better of each player is!
• Completionists get something else to complete: unlocking every upgrade!
• After getting each annoying upgrade from map currency vendors enough times, if you use those to unlock, you don't have to get grind for each again, you go grind for a different one.
• People who love testing new builds don't have to spend little fortunes making gear sets, getting more upgrades or using upgrade extractors.
• If templates get eventually added, if both upgrades and stats become unlocks, loading previously saved builds becomes easier and less reliant in having many pieces of gear ready in your inventory.
• Current systems like the wardrobe, salvaging and the trading post still work with the system.
• Legendary weapons get an additional benefit on top of all stats: All sigils and runes.

The only downside is upgrade extractors becoming pointless.