Any updates? Arriving early in the morning from the US, have two hours before a connecting flight. How long is the process taking?
The biggest factor is the number of flights arriving carrying primarily non EU passengers however Lisbon airport along with Porto really are proving to be wholly inefficient especially when compared to their neighbour Spain.
It's impossible to give an estimate on how long the process might take because there are so many factors involved. There's nothing you can do that will have any bearing on the process so you'll just have to accept that it will be what it will be.
When you get into the passport area, have your passport out and do not hesitate to speak to anyone with a pink or orange vest and tell them your connecting flight. No real language skill is needed here, just say 'Sevilla' or 'Malaga' or whatever...
And then, KEEP advocating for yourself. We jumped the line back in April due to a short connection.
I echo @skunklet1771's comments to be ready and to be your own advocate.
We dealt with the reverse at LIS (BCN->LIS-->IAD) in May where we were with many arriving connecting flights trying to work through the EES exit process to get to our international flights.
Two things "helped" us - the US leg was slightly delayed departing (+30min) and the airline staff (TAP airlines) grabbing folks with tight connections and ushering them to the front. Even with the help, it was tight, disorganized, and a bit of a frenzy. Often, also, changing instructions from the various staff working in the process made it more challenging. My bet is plenty of folks missed connections - and a good portion of them because they simply went with the "flow" rather than paying attention and working on figuring out how to get through in time.
The process should not require such a level of uncertainty (and stress), and hopefully it's being further improved every day. To me, two hours is about what I would feel comfortable with nowadays - but I also think your flight might arrive early and/or before many others arrive as well, so you might have a much different experience than we had with an afternoon flight and many flights arriving on top of each other.