The consequence of having a deep story is that the sex often gets in the way. This was certainly the case in the second half of this, when the MC ran through half a lifetime of pussy, and it made any choice of LI to the exclusion of others nonsensical.
They would've done well to finish this in 2 or 3 fewer updates, and cutting back on some redundant sex would've helped.
Chandra was always going to end up being a side piece- it's how she was set up from the start- just as Sonja was always set up to be nothing but the ex, backslide notwithstanding.
I would speculate that the dev has grander plans for Chandra in a continuance of this saga and needed to keep her unhitched.
That said, this was brilliant.