Traveling from Upminster brige to baker street is close coming up to 1
hour 45 mins compared to a while ago to 1 hour and ten due to the fact
of delays and longer routes.
I find my self taking buses as its quicker yes buses being quicker!

During the current weekend closures, you could try getting the c2c
service from Upminster station to Fenchurch Street, then walk to
Aldgate East and get the "enchanced" Hammersmith & City from there to
Baker Street.

Having said that, the engineering closures do seem to be getting
worse. Half the underground seems to be closed at weekends these days.
There are some particularly badly-coordinated ones as well: for a
couple of Sundays last month (13th and 20th), much of NW London was
cut off from the centre, due to 3 separate sets of engineering works
resulting in the Metropolitan, Jubilee, Bakerloo, Chiltern, and
Silverlink Metro all simultaneously having no service to central
London.