One thing to think about is that what you want to accomplish is having your manager look forward to talking to you instead of dreading it. This is especially true as you start these.
So first talk about the projects neutrally. Do not start in on a litany of complaints, particularly complaints you know he or she can't do anything about like the ridiculous deadline that came down from above or from the client. You can bring up roadblocks if you want or if the conversation naturally goes there, just don't make everything you say be negative.
If you have process changes you want to make, start small. Don't go in there with 23 complicated, hard-to-manage, different changes that you just have to have have immediately. Find something easy to change, and write up exactly what the change is and exactly how to do it and then present that. Once you have a few successes under your belt, you can go for more difficult things.
Remember that not only are you talking to your boss, but so are your teammates. If you have differing ideas about what you want to accomplish, then the boss can't make everyone happy all the time. This means that at least some of the time, you are not going to hear the answer you want to hear. Take it gracefully. Do not keep pushing for things once a decision has been made. Bosses do not listen well to sore losers. There will be another time when you win. You need to have patience to affect the workplace positively. So think about that when talking to your boss.
If at all possible, try to have some good news about progress made on something or something that happened that you liked. Nobody wants to talk to Negative Nick or Negative Nancy. You will find that the problems you have will be given more attention and be taken more seriously if problems are only a small bit of what you talk about. If everything you say is a complaint, then your boss is going to just dismiss what you say as you being a person with a poor attitude.
If your boss did something good since the last meeting, say thank you. "Thank you for clearing up that problem with the QA department" or whatever roadblock they cleared can go along way towards making the boss feel better about you. Bosses are people too, they too prefer to deal with people who appreciate them.
Ask about neutral informational type things some too. No one is going to hate you for asking about when you are going to get the new benefits info for next year or how is the search for a new building coming along. If there is something they likely can't talk about like a layoff, then don't persist in asking about the subject after you were told not to. Know what kinds of things they as managers have to keep confidential and don't try to wheedle the information out of the boss.
If there is a performance problem with someone on the team, you can bring this up to let them know there is a problem (as long as you don't point out that everyone on the team is bad and only you are good). But do not expect to get any information at all after that about what was done or what HR had to say. You wouldn't want others to know if you got reprimanded or suspended or put on a performance improvement plan. And it is none of your business what management and HR decided to do about a problem even if you brought it up.
Bosses tend to listen more to the people who produce. So be a producer. Then worry about process and changes.
Let the boss guide the conversation a bit in the direction he or she wants to take it. But don't think that because he/she asked you, "Do you have any problems?" that you should hit him/her with a list of 37. Limit yourself to the 2 or 3 of the most critical or something that is easy for him or her to fix.