Agents are in some instances not giving rewards, not giving necessary items to complete and sometimes reseting the mission. This is being worked on. Some have also lost some of their Agents due to the standing changes. This is also being investigated. There are some incidents reported that Agents are giving out lots of rewards too - but understandably I ain't ... uhm ... nobody is reporting that. And if it comes in we'll put a low priority on it. At least until I get that uber-battleship blueprint :P
NPC Pirates are very very very difficult. This is intentional and they will stay this difficult. What is however a problem is the distribution of them, there are too many of the "very very very" difficult systems as opposed to the "very very", the "very" and the "plain" difficult systems. Thats why you see loads of pirates defending Jaspet (yeah, I hate that too btw!!) This is being worked on - this includes ore distribution as part of the whole "distribution" thing.
Afterburners, MWD's and other items were changed. Remember to use the correct item for your class of ship, else an MWD will work as an Afterburner. Other items were also changed to better align with Tech Level II. This is intentional but this might see some further tuning since this of course affects travel time greatly. However, if you are a big traveler, use cruisers, they are nifty little things ;-)
And on Tech Level II it is in, but don't expect it on the market yet. Items will be available as soon as players sell or manufacture them. Use your agents (they aren't always broken) to get blueprints and other ingredients for the manufacturing. If you don't like doing agent missions, just wait for the players that do to sell their rewards ;-)