40KTW will be a Total War game, not a TT game. With that in mind, if CA can make something work, they will either use it, maybe slightly change it to suit the TW engine or simply not use it. It won't be an issue.

Many of the existing issues that are present in fantasy are the direct result of a fan base that was just happy to see a dead universe revisited. Any poorly implemented ideas would just be hand waved by that segment of the population, because they were just excited to be in the world of the living again. When legitimate issues were raised early on in the trilogy they were the ones doing the bulk of the damage control and spin. When new ways to express units in a way that was more faithful to the source material, they were there to temper (silence) those expectations. 

Fortunately, CA found their footing and eventually started "making right what went wrong" by game three. Unfortunately, the earlier decisions have had a ripple effect on the game's design and the ability to make corrections to its course as new ideas inevitably spring forth. That's why getting the idea of what the game is, is so important to establish before the game is even in a playable state. Questions need to be asked and answered by people that don't always agree on the best path forward.

Does a model with four arms that's holding four melee weapons make four separate attacks? If something like four sequential attacks is quite powerful, does it need to be changed to a single attack or does it require a different cost to be added to units that have four melee attacks per activation? Does the melee attack vs melee defense calculation make an appearance in the 40K universe? Lots of questions and answers need to be thoroughly analyzed if this alleged game is going to have the level of success that eluded fantasy. 

I ESPECIALLY hope that the "Physical Resistance is bypassed by Magical Attacks" paradigm from fantasy, never finds its way into 40k. Physical Resistance would have been a nice way to represent a unit's toughness or durability even in the absence of armor. However, because magical attacks made that potential durability invalid, it limited the usefulness of Physical Resistance. Suddenly, a unit wasn't tough anymore because the unit striking it had magical attacks. That's pretty limp. 

The system itself is not worthy of being tossed in the trash. It does need to be expanded on, though.