BitShares pros:
- The most scalable in-memory blockchain
- Monetisation of issued assets using custom fees
- Really fast 1.5 sec average conformation no matter what is your tx about
- Smartcoins (bitUSD, bitCNY, bitEUR) allow to build trustless processes with off-line businesses
- Forward thinking community
- Built-in referral program
- Community client is built for in-browser use on steroids (web-sockets + react)
- Network explorer (Cryptofresh.com) will be open-sourced soon
- Fast adoption signals
- Truly decentralized blockchain self-paid development team
- Technological certainty as Bitshares already passed the most hard iterations trying to find minimum lovable product
- DPoS

BitShares cons
- Currently smartcoins have low liquidity
- Currently multisig don't work in clent
- No asset-based voting and account control
- No ability to create assets with locked supply. UIA are always issuer dependent in some sense.

NXT pros:
- Convenient Phasing and Account control allow you to build highly customized processes
- Data Storage, Marketplace

NXT cons:
- No ability to monetize assets through custom fees
- Very slow in comparison with BitShares and slow in comparison with Ethereum
- Stagnating community and network activity
- Development and consensus through BDFL model (with all honour to Jean-Luc)
- Weak improvement process: If you develop custom soft, so get ready for sudden API changes
- Huge uncertainty caused by NXT 2.0
- Naive PoS

Summing up if you need asset with exchange without all bells and whistles of NXT (alias, data storage, marketplace) go BitShares. If ability to build sophisticated asset-based voting processes is crucial for your use case go NXT. Otherwise go BitShares.

If you need really deep custom things go Ethereum (much custom, significantly slower than BitShares but much more faster than NXT)