You know, most cryptocurrencies have flaws. Here are a few:

Blockchain scalability (size of blockchain)
Network scalability
Premining
Requirement of being online to make any sort of payment.
Lost/Stolen Keys
Practicality
Danger of third party holding your wallet/keys on your behalf
Adoption from wider public
Viruses relating to cryptocurrencies
Actual implementation (inc. possible flaws in protocols and implementation choices; [language & libraries etc.])
Portability of underlying software (to new architectures/operating systems)
Mining often in practice requires joining a pool, which is sometimes centralised
Use-value vs economic value hyper-inflated.
Regulation
New coins solving mentioned problems unlikely to be added to any real exchange short-term.

... in addition...

For mined currencies:
Mining needing specialist hardware in practice
Energy use of mining

For the consensus-based currencies:
Sibyl attacks
Making rich richer (interest is given as a % to those already with coins)