1. Standardization in regards of (globally) unique identifiers and ontologies. Most things un the semantic web have multiple identifiers and, based on personal preferences, attributes linked to different ontologies. There's several projects that try to gather data for the same thing from various ontologies, but sometimes the same attributes have differing values because of conversions or simply extracting data points from different publications where different methods have been used to measure stuff.
2. Performance of large datasets gets really bad since distributing graphs is still a problem that lacks good solutions. One of the solutions is to store data in distributed column stores. But there's still a ton of unsolved graph traversal performance issues.
I strongly believe that the technological batriers need to be solved first. Until then there will always be the person in meetings, asking why not use relational or NoSql tech because of performance...