A network engineer can list a number of issues you can potentially run when using STP protocol in your switch network. Over the years the network industry has created successor protocols like RSTP or MSTP. Both are improvements and offer much better convergence time and respond much quicker to switch topology changes. One of the major disadvantages for networks that relay on STP is the fact that they don't support multipathing. It means once network topology converges there will be blocked path between switches that are elected and managed by STP. This often redundant links can't be used because of a loop risk.
But there are better solutions today on the market to design better layer 2 Ethernet networks (more scalable, with higher throughput and with active link redundancy as an example). The 2 most popular are based on SPB and TRILL protocols. Both of them are used as a foundation in switch fabrics products. To better understand both of them the pictures below provide a side by side comparison. This was taken from Avaya document: Compare and Contrast SPB and TRILL.
Avaya is a SPB promoted so the comparison is a bit waited towards SPB but nevertheless it gives some inside view into both protocols.