I wouldn't say it's soulless exactly, but is still lacking the glue to hold it together as an experience (but that has improved from 1.4.2, when I first played).
Generated companions rather than crafted ones - that has some impact, but less because Warband's companions were particularly well crafted than because as players, we became used to them over multiple playthroughs, which is a little unfair on the generated ones. I have become attached to some companions more than others, but until death rates are reduced, its easier to send almost all of them out as caravans - with zero attachment.
The faction-clan system would be improved in terms of 'soul' if (as others have suggested), you also had a relation with individuals within a clan, rather than the clan as a whole. If you can receive significant boosts to relations from helping a party in a battle, or giving them a bit of cash or doing a quest, maybe traits should also have a bigger impact rather +1/-1 per trait and/or be a constant modifying positive or negative tendency to your relationship.
Some balancing of the levelling/skills/perks would help, to avoid having to focus on it as a logistical and mathematical problem rather than an intuitive reflection of your character.
Mostly though, soul will come from play decisions and execution having consequences. Overall game pacing needs improving (my biggest bugbear, renown gain needs a game setup config option; I can be clan tier 6 and Calradia's superpower by the starting character's mid 30s, and I'm not that good at the game - multi-generational play, which would also add 'soul', therefore doesn't really exist yet). Currently, building up can be interesting, establishing your kingdom becomes a bit manic, then once you start recruiting lords it's just an inevitability that you will rule Calradia, if you can be bothered.
Oh, and of course battles need to be a bit slower (better armour ratings). High death rates means a temptation to use auto-resolve too often, which removes a feeling of connection. I had a battle a few days ago, where I got knocked out fairly early, with 2,400 vs 2,500 - I lost, with the enemy ending with just 8 soldiers remaining. That adds soul. But I think I save scummed as 6 or 7 lords/family/companions were killed.