I also suggest that perhaps we can have MTF scenes on occasion like that on other monitors to give the impression of MTF soldiers making their way through the facility doing their job of securing it. It would also serve as an early warning to the player if an MTF soldier is approaching their area.
I would also like to see a security room where most of the monitors are located for 'ONLY' monitoring the facility and not containment cells. The monitors used for containment cells should be at the location of the cell itself. Perhaps the captain of Epsilon 11 could position himself there, feeding the other MTF soldiers with information on your location as well as other SCPs, survivor holdouts etc... The power room may be more important with this idea since disabling the cameras could be useful to keep the MTF soldiers from finding the player as quickly.
The MTF should also be seen interracting with SCPs, especially escaped ones. I would like to see 096 reacting to an MTF if he is unfortunate enough to see its face. However, it should not be easy as I would assume they are the best at what they do. They wouldn't make such mistakes easily. I would like to see perhaps an MTF being seen by the player being dragged off by 106. That also would be cool.
Here is my last idea about MTFs so I don't bog you down with information overload. I would like to see the MTF soldiers progressively reduce in number. For instance. They are called Nine Tailed Fox because there are nine members to the squad, correct? Well what if they start off as nine but as a few get picked off here and there by 173, 096 and 106, they become fewer in number. This would give the player a little more of a fighting chance to escape them and perhaps escape the facility if they can last that long. I would suggest no fewer than 5 should die. I imagine the difficulty level with this idea would appear more like a pyramid. The difficulty starts off low since the player is dealing mostly with SCP 173 and 106 mostly. Then it rises to a peak when the MTF's show up in full numbers and strength. But as they began to reduce in number, the difficulty settles down a bit to allow the player to progress. Anyway, its just an idea.
1 and 2 disagree. I would rather see updates with the MTF's interacting with the SCP's like in your third suggestion.
In additon to SCP-096, I have a few other SCP's I'd like them to interact with.
SCP-008: MTF units attempt to close the leaked container if the player has not already contained it.
SCP-049: MTF units terminate the two instances of SCP-049-2 and try to sedate SCP-049, whereupon they will return him to his containment chamber and close it.
SCP-035: If the player hasn't freed SCP-035, MTF units will activate the decontamination gas and terminate the possessed scientist before returning SCP-035 to its glass case.