I haven't really messed with Memory Alpha much, so it could be that the items I've seen on the vendors won't work for it.
That said, I've found Mk IV and Mk VI phasers on vendors at Starbase 39. They run about 1k each.
That leads me to one of three conclussions:
1- Those items are not used in Memory Alpha crafting.
2- Those items are used in Memory Alpha and those people saying they aren't available on vendors simply haven't found them yet.
3- Those items are used in Memory Alpha and those people saying they aren't available on vendors are buying them themselves and putting them on the exchange for 100k.
I honestly do not know which of these is the case, but if I were you, I'd make a list of what you needed and hit SB39 (Sierra System, Alpha Centauri Sector) and see if you can find them there. It may be a futile effort, but it's worth a shot. =)
There is nothing wrong with the STO crafting system because there is no STO crafting system, nor should there be one. What we have is a requisition process for upgrading looted common items. It's that simple and they don't need to fix it because there is nothing to fix.
I'm not really sure why you think crafting is so bad. I think its a good thing to give folks something to do outside of missions and whatnot. Some people just like to put together pixels to make cooler pixels. I'm all for a good crafting revamp.