They are not critical design flaws.
Dying servers is only a problem if you don't use your own domain. We're in an intermediary period; more people and orgs will run their own servers in the future
Scalability isn't a problem reserved for AP. Fanout of messages to thousands of recipients takes time and resources. True in siloed networks as well as federated.
Search is not a technical but a cultural issue in the fediverse.