I am writing a thesis and I frequently find my self using the phrase 'is that'.
For example: "The other feature that has been neglected is that the expert system would ..."
I have been told that this is ugly.
What are some alternatives?
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The list is nearly endless:
The expert system farkling the foo is another feature which has been neglected.
Also a neglected feature, the expert system will farkle the foo.
An additional neglected feature of the expert system is farkling the foo.
Farkling the foo is the other feature of the expert system which has been neglected.
Farkling the foo is the other neglected feature of the expert system.
The alternative is to stop listening to people who say silly things like that.
There is, unfortunately, a sub-culture of writers who obsess over the minutia of prose without having any actually stylistic skill. This means that come up with a collection of vacuous rules, and one of the most vacuous of these is a suspicion of any form of repetition. If they can find the same course of three words three times on the same page the are instantly aroused, like a pointer who detects the smell of game.
The only place in which concerns could be legitimate at all is in literature. For the most part they don't apply in literature because they are just simply wrong, the product of people trying to do by simple rules what can only be achieved by mature taste.
In academic and technical writing, your overwhelming obligation is to be clear. The use of "is that" in the sentence, "The other feature that has been neglected is that the expert system would ..." is clear. That is all the virtue that it needs to justify its use.
Trying to come up will alternative is quite likely to make your prose less clear, which is the cardinal sin of academic and technical writing. Familiarity and repetition are important component of clarity. Saying the same thing the same way is an important aid to clarity. Rather than trying to introduce variation here, you should be trying to eliminate it.
Variety may have a role to play in art; consistency is fundamental to commerce, engineering, and academic study.
It might help if you try always to look for an active verb, and an active way of phrasing your statements. "Be" verbs (is, are) lie flat and motionless.
"The problem with this approach is that...." is a weak way to start identifying a problem. Instead, try an active verb -- don't just say 'this is a problem" but "this thing does something (which is obviously a problem)."
"The approach (fails, misses, lacks, hurts, ignores, minimizes)" and so on.
As mentioned by others, also, the use of "is that" is awkward (ungrammatical?) in your example.
"The other feature that has been neglected is [X feature]..."
"The other feature that has been neglected is that [there is a feature named X]
In other words, basic recasting of your sentences can eliminate "is that" in most cases.