Well I shall do my best to answer your questions here.
We'll start off with the weapons and twin-linked questions. As you've quoted the rules, refer to this sentence:
Quote:
No model can pick the same item twice, and all equipment, other than wargear (which is assumed to be integrated), must be represented on the model.
So we have a rule, stating that no system can be taken twice. So if you wanted to take 2 Plasma Rifle's, well that sentence right there prevents you from doing that.
So then we look down at the next section for Twin-linked battlesuit weapons systems. We have an additional rule that modifies the above restriction in very specific ways. Weapons systems that have 2 point values, can be taken twice but they count as being twin-linked. It then goes to say that the twin-linked weapon counts as 2 weapons systems. GW is known for this type of writing, and it appears throughout their rules. They will give an overall general restriction, but will occasionally allow a bypass of that via a specific way.
So all the forums that assume they are twin-linked when buying 2 weapons systems are correct. You really can't use Shadowsun as an example as 1. her suit is completely different from the normal crisis suits and 2. one unit's options are not always the same as another unit, nor are the restrictions.
So for your next questions about drone controllers. This is answered by reading the description for the Drone Controller (pg26)
Quote:
A model with a drone controller must take one or two Gun, Marker, or Shield Drones, in any combination, from the Wargear list.
So that answers it for you. If you take a Drone Controller, you can take up to 2 Drones with that suit.
And now on to your third question. Actually, they are the same system. Look under the
Hard-wired systems section.
Quote:
The same rules apply to the system whether it is hard-wired or hard-point mounted.
This says that regardless of whether you take a mounted Drone Controller or a Hard-wired Drone Controller, they are still the same system and thus you can not take more than 1 of them.
I hope that answers your questions. Learning the game can be quite a challenge, as GW isn't exactly known for being very clear on how they write their rules. We'll do our best to answer any other questions you have in the future.