Hmm Always difficult to say what makes a good anime, as you think you like or don't like something then you look at your favourites and they isn't what you said you liked/disliked. But here's an attempt.
-Simple concept, complex execution. The concept of the show is best if simple, revenge, getting home, getting money so you are never in any doubt as to the main important things. The Execution of the concept, how they get their revenge, or the scam to get the money should be complicated and always keep you guessing. Hate guessing how people are going to do things 30 seconds after they work out how they are going to do them. Likewise with characters being able to sum them up quickly is good, but understanding them takes more.
-Realistic responses , take your average male high school student and shove a scantily clad girl in front of him and you'll get a mixture of embarrassment and trying to see as much as you can. Not either the twin red geezers or dropping jaws and eye's popping out. Put him in a battle situation he'll freak out. Also love it when character echo my thought's (ie say what I would have said). Also helps if the have more than two emotions.
Causality You do something in one episode and it has effects throught the series. Not necessarily meaning it has to be a serial plot (like Rahxephon or Gundams), don't like it when the reset button is pushed at the end of every episode, and you can practically watch the episodes in any order.
Well thought out world - If you're going to have magic, alchemy, hyper technology, mecha, space ships please of the rules for them first. If you can teleport from anywhere to anywhere why have cars or any other from of transport, if you can make anything with alchemy why not make everything with alchemy and have no factories or craftsmen?
Crossing genre's- Just becasue you are writing a serious drama doesn't mean you need every one to be serious all the time, like wise if you can inject a little drama or seriousness into a comedy it improves it. Best to give an example, in Marhormatic you where always reminded at the end of every episode that she was going to die. Conversely Batuo's humour often helped make the series/movies more enjoyable. Thing is it has to be woven into the show, not just a 'joke episode' or serious ending to a comedy series.
Other things like Good and Consistent Production Value's are also important... just not very interesting to talk about. Attention to Detail especially things like blinking, it just really bugs me when they don't blink. Also it's nice if they have more than one thing in their wardrobe.
