Some things I don't love:
* A lot of the integrations seem half-baked or to not quite fit the generic Lovelace cards. I think to some extent this is an inherent problem in supporting a lot of devices that have crappy, non-standardized APIs. Example: if I bump up the low temp on my Venstar thermostat on the Home Assistant dashboard, Home Assistant will immediately set it back. If I dig through logs, I see the thermostat complained that in auto mode (heating or cooling as needed), the low set point and the high set point have to be (at least) six degrees apart. When I adjust the thermostat through its own touch screen, the high set point automatically raises to meet that constraint. Home Assistant should do the same. I've been meaning to look into fixing it myself, but there seem to be weird things like this on every integration.
* You need multiple automation rules to do almost anything. I think it's common to want the state of one thing to match another (for example, garage door open => sticky notification on my phone, person in driveway after sunset within last 5 minutes or switch on => driveway light on). You need a rule in their YAML DSL to for the off->on transition and another for the on->off. It'd be nice to set a rule that defines a level rather than an edge and have it internally do the transformation. It'd also be nice to define the actions of a notification's buttons inline, rather than as a separate automation.
* The companion Android app's notifications seem to be flaky. At least, they're sometimes slow. I think they can be delivered out of order and possibly are lossy, which aggravates the problem with not having something that just sets the state reliably. I assume it's pretty hopeless to have it reliably be in the right state if your phone was off when a notification was supposed to be delivered or Home Assistant was down on state transition or the like.
* Some things seem to be only checked at startup, so my house has race conditions after power outages. For example, if Home Assistant starts up more quickly than my Yamaha AV receiver (+ network switch + DHCP server), I can't control my home theater setup until I restart Home Assistant.