When creating an IFR route, should one route around and avoid class B airspace? Should one include the IAF (Initial Approach Fix) of the desired IAP (Instrument approach Procedure) in your route? Should one include the desired STAR and/or SID in the comment section or route section?
You don't need to. If enter a start & end point at https://skyvector.com/, it can suggest standard routings for you. You can follow those, or tweak it up some. For example, 6B6 to WWD, standard routing will put you on V1 and will take you out over the water quite a ways, farther than I prefer to be in my single engine 4 seater. I'd tweak that to route over JFK, Colts Neck VOR, Atlantic City instead, having been cleared for that route several times by NYC approach. IFR at 6000, and VFR even, at 6500 feet.
I've also talked to pilots going north & eastbound who were IFR and routed north around the NYC Class B, sometimes quite a few miles out of the way. So it really depends on what the weather is doing and how busy the Class B is at the time of your transition.
For the approach part, I'd leave that out as conditions can change and your approach will be determined by the weather at the landing end and ATC will assign what to use as you get closer, or you can request a Visual Approach if the weather is nice and you don't need the approach. One thing you can do is put "No SID, No STAR" in your flight plan if you don't have them on hand.