I hear that sentiment a lot (I blogged about it here: [1]). Basically, "every time I use Sinatra, I ended up with franken-rails" means that Sinatra was either picked for the wrong reasons or misused. If you want to build something large based on Sinatra, for the love of $deity, please use organization systems people have built for you, be it Padrino, some Sinatra stack or something else. It doesn't mean that Sinatra is bad, but its often misunderstood.
[1]: http://www.asquera.de/opensource/2012/10/22/the-rails-monoth...