Pilots are always a bit ropey, they try to cram all the story into an hour to set up the premise, I'm more forgiving of pilots than the rest of the first few episodes, I understand why they did it but I feel starting with the Wayne murders was a mistake, I'd have left it to the mid season finale (maybe season finale if it didn't feel like it dragged on).
I don't know if it's just the fact that I've seen that particular couple die like a hundred different times or the general apathy of watching tv show characters that are only in their death scene, die. I mean if this was your average procedural cop show, I wouldn't even remember those peoples name after that episode is over. I feel like you have to get to know a character to give a shit when they die, they seem to be going for the recent cannon that the Waynes are killed to send a message or were cleaning up the city too much, rather than a random street mugging gone wrong, so show it, even if it's just in 2 or 3 scenes it'll be better than nothing. Get Gordon and Thomas to be pals or strike up some rapport as their paths cross, you can grow an attachment to a character that you know is fated to doom if you don't jerk the audience around over long period of time. Sure, you'll never get the shock value that say, game of thrones will get you but it'll have greater weight than victim of the week that they were.
I think the only ones that nailed it and seemed comfortable in their role was young Bruce (watch the bit where he says 'I'm glad he's not dead') and maybe Oswalt but he was just chewing the scenery for 80% of the time so not as impressive, I might watch it again to get a more measured look at it.
I liked it though, considering I usually hate time travel or prequels that's pretty good in my books.