Perhaps an in game mechanic that takes the place of an invisiblity function where the user is temporarily visible. This function could have a small battery attached which is drained by the energy taken to be visible and the user must streamline their actions to manipulate certain environements whilst visible.
For example:
The protagonsit must access a location, the entry of which is monitored by both video and thermal security devices, the user must stealthily collect the tools needed to access the facility but they must be visible whilst doing it as the system compares the protagonists visible actions to their invisible ones. There are blind spots in which the protagonist can stand to recharge their visiblity batteries but clothes hovering in the air around an invisible body are conspicuous so the player must choose their invisible moments carefuly.
The player may neeed a key card, some form of Biometric ID and perhaps a password which he can pick up from other people by stealthing up to the NPCs and using slight of hand and confidence to gain the NPC's data. Once inside the facility the player must find a place to stash his clothes until it is time to leave.
As for the issue of Block and Tackle perhaps the protagonist could where a carbon nanotube, low visiblity, body stocking for protection. This would have the added effect of making the protagonist highly resistant to cuts and scrapes where his blood may show up his passing or his location.