AMTK1007 has made some important points, but I thought I would try to show why the direct path will not happen.
First, it is a dead letter. The state is already committed to the Milwaukee - Watertown - Madison route. It has purchased the Watertown - Madison line and completed the environmental impact process as well as preliminary engineering.
Second, the Madison - Milwaukee connection is at least as important as the one to Chicago. It provides better access to air travel via the Mitchell Field station. Thus the Milwaukee routing will generate more potential trips and better justify the expense of the upgrade and multiple frequencies.
Third, the direct route isn't dramatically shorter, cheaper, or faster. There are two possible direct routes from Chicago, one that follows the same route as the Metra Milw. District- North (MD-W) and the WSOR to Janesville, or one that follows the Metra UP-MW route and the UP to Janesville. (There may be a possiblity of connecting to the route used by the Metra NCS line which passes O'Hare, replacing the lost airport connection.) From Janesville there are also two options: 1) WSOR to Milton, Edgerton, Stoughton, and McFarland or 2) the UP to Evansville then along a rail banked line to Oregon and the south side of Madison. Both lines meet crossing Monona bay then pass the state capitol before hitting the line to Portage, La Crosse , and St. Paul, with the station stop at airport. I don't have the actual distance along this route, but my guess would be that it is about 30 miles shorter to Chicago. The more extended trip through Madison negates much of the length advantage, and the Madison - Janesville segments aren't very straight. It would likely cost similar amounts to upgrade the line from Madison to the end of the chosen Metra route and build new stations.
[There are a few advantages, the station could be built in downtown Madison with better access to the goverment, university, and business activities as well as more central location for Madison residents and a somewhat shortened trip time to Chicago. This shortened time would likely be given back reaching the airport site for through trains to the Twin Cities. A central Madison station would have a higher cost and more difficult parking, and the planned commuter service could complicate things.]
Fourth, by skipping Milwaukee, the direct connection complicates train options from Chicago to the Twin Cities. The existing plan envisions a "110 mph mainline" Chicago - Milwaukee - Madison - La Crosse - St. Paul and assumes that all corridor trains will use it, no divergences. If you build the Madison - Janesville - Chicago route then which way to trains from the Twin Cities reach Chicago? The travel demand from the Twin Cities to Milwaukee is likely higher than to Madison, so most trains would go directly to Milwaukee, so the whole CP mainline would be upgraded to 110 mph. For the handfull of trains between Madison and St. Paul the CP Portage-Madison sub-division would have to be fixed-up for at least 79 mph passenger service, and perhaps all the way to 110 mph. None of this would satisfy the demand for Madison to Milwaukee service, and a fast line close by at Watertown, so there would be demand to upgrade from Madison to Watertown as was done to Portage. Now you've built a system with two paths from St. Paul to Chicago, via Madison and via Milwaukee (or three if you duplicate the current plan for via both), and all of the upgraded lines of the current plan, plus, upgraded lines between Watertown and Portage via Columbus and Madison and Chicago via Janesville that are unnessary to operate the system effectively.
Summary: The benifits of such a routing are few and modest (slightly faster to Madison from Chicago, potential of centrally located station in Madison, HSR to Janesville) and the costs are rather high (no Madison - Milwuakee without additional investment, which way to St. Paul?, extra trackage required, etc.)
Post Script If what you really desire is service to Janesville and vacinity there are a few options:
1) traditional commuter service (minimal or non-existant reverse commute or mid-day service) through a Metra UP-NW extension (jurisdictional issues)
2) Rockford - Beloit - Janesville, full day, bi-directional commuter/ local service. These cities are decent sized and fairly close together. Not sure of track availability though. Jurisdictional issues would exist.
3) Extend a (conventional) Blackhawk train (one not going to Dubuque) through Beloit and Janesville to Madison. This would connect Janesville, Beloit and Rockford to Madison by rail as well as Beloit and Janesville with Chicago. Best tried after one of the commuter options above has improved tracks and/or stations, and there is Milwaukee-Madison service.