For the most part enterprise apps do suck. But I imagine there are enterprise apps that are just amazing. The software that allows UPS/Fedex to deliver packages so efficiently must be fantastic. Or the stuff that powers the supply chain of Walmart, or the stuff that powers Amazon.com's ecommerce. It'd be great if someone could share insights from real world examples of enterprise software that works amazingly well.
Those examples are different because they are core to each of those companies' business model by being directly tied into their revenue stream. Simply put, it makes them competitive. Therefore, those apps you mentioned have to be good if not better than what their competitor uses.
The problem is more about internal applications that have nothing to do with the identity of the company itself. Personnel management, time tracking, accounting, and payroll apps suffer from poor quality if built in-house because they are part of the cost of doing business independent of what that business may be.
And that's the irony of it. Why do companies think they are going to innovate in the area of personnel management, time tracking, accounting and payroll in such a way that it'll give them an advantage over their competitors who also need to do this? These are commodity processes, or should be, and should be deployed from proven, mature technologies. The fact that they are commodities means they should be cheap. The fact that this isn't the case means this industry is broken (again most likely because the people tasked with deploying these processes/services are not going to be the ones using them).
I consulted for a few hours on a very enterprisey project involving UPS RoadNet Transportation Suite last year. RTS is used by the big company I worked for to plan truck-driving routes. Note: this is a more ambitious technical challenge than anything we did in-house. The major thrust of the project was reconciling the logistics team's desire to work together with IS's desire to simplify desktop management and IS's desire to isolate everything from everything else (for security reasons!).
Our users were satisfied with RTS's planning results. The UI gave them some trouble. The major dissatisfaction with it was the difficulty in updating/maintaining the many desktops at our company and at our partners' offices. A year ago, word was that UPS was considering possibly offering RTS as a hosted service.
So, is RTS amazing? Well I haven't seen any papers from UPS computer scientists describing their novel contributions to the algorithmic state of the art. The UI is a bit clunky; users don't fall in love with it. But, it doesn't crash often and it does a satisfactory job solving a non-trivial problem, which is more than I can say for typical in-house enterprise software.