I guess I never responded with my own thoughts about the Houserule in general.
First up, I understand where you're coming from (and pretty much agree with just about everything Quatar just said). But I also think Limits are a great mechanic that just needs tweaking. Having also transitioned from 4th to 5th edition, I still remember the sort of dicepool shenanigans that would crop up. I don't remember exactly where I heard it, but back when 5th was first coming out I remember someone making an example of why Limits as a mechanic was a good idea:
Imagine, for a moment, you have two characters with very different skill sets both trying to shoot a Pistol. One is Untrained in Pistols, but has a decent Agility to compensate, and bought the best gun on the market with all the custom molding and gadgets to make him better at shooting. (Pistols 0, Agility 4). The other is equally Agile, but is well trained in firearms and doesn't believe in those fancy gadgets, he's just using the loaner gun at the shooting range. (Pistols 4, Agility 4)
Now, in 4th edition, those gadgets would have given a dicepool bonus to our untrained shooter, giving him a higher dicepool, and the crappy inaccurate gun that is beaten up would give a penalty resulting in the two having the same total dice pool of around 6-7. So by that logic the two of them end up being just as good as one another.
In 5th edition, the tides change. That crappy gun is really just inaccurate, so it gets a hit to the Limit of the Pistol (lowering it down to 3), and all those gadgets primarily just give an accuracy boost (and only a minor bonus to the dice). The final results here are: Untrained at 4 dice [Acc 7], and Trained at 8 dice [Acc 3].
The 5th edition mechanics end up with something that really does more closely match what you would expect in real life. The guy who has never handled a gun before, even with targeting assist is going to have trouble hitting the target accurately, while the well-trained shooter is going to be hitting the target regularly even with a crap gun. I mean, at a shooting range, stationary targets would probably range in threshold from 1 to 3, maybe 4 at the most. So that trained shooter takes a second to Take Aim and they have the Accuracy to hit any of that.
Overall, that analogy really works for me as why Limits are a good idea. It also gives a way for items and effects to give different kinds of bonuses for different causes. Where before it was all just lumped into "here's +4 dice."
Now, like I said before, I do think there are some tweaks that could be made. Personally, I always thought that melee weapons have accuracy ratings that are a bit too low (particularly when you factor in that there are very few ways to increase that accuracy). I thought a good fix for that would be for Melee either a) use the weapon's Accuracy or user's Physical Limit, whichever is higher; or b) make melee weapon accuracy a modifier to the user's Physical Limit (for example inaccurate weapons would be a -2 limit, while extremely accurate ones would be +2). Between those, my preference is the latter and the guideline I generally use is subtract 5 from the melee weapon accuracy before adding your Physical limit.
Thinking about that, you could make a similar alteration to Matrix limits. I never really thought about it until now, but why doesn't a user's Mental Limit apply to Matrix actions at all? You could use the same formula even, Mental Limit + Gear Limit - 5. And that would work for the idea of particularly gifted hackers not needing a deck for some actions. Although I'm still a bit wary of that, maybe make that one a bigger penalty to the total, or require a quality to be able to do an action without needing to have the Sleaze or Attack rating (like Jurryrigger).