Whatever you do, don't buy the e-book releases most recently introduced; they are HORRIBLE copies filled with words that are run together, misspelled, and slaughtered with mispunctuation. I am normally not that big a grammar cop, but holy crap, they are awful. Every page, it seems, I am running into something that forces me to re-read the sentence a few times to understand it.
They read like something that was orally dictated to a computer, with no editing or spellchecking afterward.
One of these days...possibly soon...I might make my own digital copies of all the out-of-print Battletech novels in some sort of e-book format, so people who do not have the cash or desire to drop over 100 bucks on the first book can actually read it...without the complete lack of editing found in the presently-available copies.
Anyway, back to the topic on-hand...I started with Twilight of the Clans, then read the FedCom Civil War books, and branched out into the past from there...so, everything I read afterward was something of a sequel. It was pretty cool, because it was like meeting the people who were already legendary in the later books. Seeing Victor Steiner-Davion as a hotheaded, somewhat ignorant youth...reading about a young man who went by the name Alek and quoted dead Russians a lot...learning about the upbringing of Theodore Kurita, and how it changed him...I would almost say it was better this way, than reading them from beginning to end.
That said...if you start on a series, and want a better idea of how the Clans differ from the IS, the Blood of Kerensky Trilogy is an excellent starting point, IMHO. Something to keep in mind with the earliest of the Battletech books is that the terminology for some things did not seem to have been set in stone yet; the IS did not have Heavy Laser technology in the 3020's, for example; they seem to use 'heavy' to refer to the Large Laser in some of the early books, as one example.
Just my $0.02, of course.