Why can some QBs take undrafted WRs and make them into stars? Who exactly has Russell Wilson had to throw to over his career? It seems some QBs like Tom Brady or Ben Roethlisburger can take just about anyone and make them better. It's not like Antonio Brown was drafted in the first round (he was a 6th rounder)... or Doug Baldwin (undrafted). 

Team stability at QB and Coach is a huge factor. Look at the turmoil the niners have had over the last 2 decades. 03-2010 was a mess. Harbaugh stabilizes things 11-14, then Tomsula and Chip Kelly dumpster fire, finally you get back on track with Lynch and Shanahan. 

Give it some time to stabilize. Shanahan/Garopolo are the real deal. Give them time. 

ALL the great organizations have stability at coach/GM/QB. I think the 49ers are just getting started. (and I'm a Seahawks fan)