Regarding threads: I like a particular brand of 100% cotton and have used it extensively, buying neutral colors that pretty much go with any fabric in my scrappy quilts. However, I'm not above grabbing a spool of old thread in a color that I need at the moment and as much as I enjoy the more expensive threads, I often use up old thread that I have on hand.
Any linting of the bobbin area of my machine is easily cleaned when I change bobbins or when I clean and oil my machines. In particular, machine quiting produces a lot of lint which I believe is due to the batting, etc., rather than the thread used in the quilting.
If I were making an "heirloom" quilt, then I might be more particular. However, most of my quilts are meant to be used and washed and used again. I believe the fabrics themselves will wear out long before I need to be concerned about what is going to happen to the threads or to the seams.
One concern about using old spools of thread is that they might be weak, due to age, etc. In that case I test the thread by pulling on a strand. If it breaks very, very easily, I toss it in the wastecan. If it is sturdy, it will do just fine. I've used threads from old wooden spools with no problems whatsoever.
One thread that I do not like to use is the polyester thread that is sold in the bargain bins. Even that is probably a decent thread to use and my dislike is personal, not based on experience.
I do like to buy colorful variegated threads for machine quilting. In that case, I'm more than happy to buy a gorgeous thread that will suit that particular quilt.
As for "heirloom quilts" ... most of us like to think that our quilts will be handed down from generation to generation. And some of them will. For the most part, if your quilt is made to be used, it WILL be used, and no amount of care will cause that quilt to last forever. It is the nature of things that all things disintegrate in time. Enjoy them now and do not be concerned that they will not last forever. I use every one of my quilts. If my kids and grandkids want them after I'm gone, fine. But I hope they use them and do not place them on a closet shelf, untouched, until the quilts disintegrate from the natural process of time.