EMB-145 FLT CREW HAS A RWY INCURSION AT MKE.

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POOR CONDITION OF PAINTED SURFACE THE SOMEWHAT REDUCED VISIBILITY; AND NIGHTTIME; COMBINED WITH NON-INTUITIVE LOCATION OF THE HOLD SHORT LINES AND SIGNAGE; DIFFICULT LIGHTING CONDITIONS INSIDE THE FLIGHT DECK; MAKING READING THE AIRPORT DIAGRAM DIFFICULT WERE ALL CONTRIBUTING FACTORS. ATIS REPORTED AS 3 MILES IN MIST; GIVEN TAXI INSTRUCTIONS OF TXWY B TO TXWY M; TO RWY 25L. AFTER WE IDENTIFIED OUR ROUTE; WE CONTINUED OUR TAXI TOWARDS THAT ROUTE. AFTER GETTING ESTABLISHED ON TXWY B; THE GROUND CONTROLLER CHANGED OUR TAXI INSTRUCTIONS TO TXWY B; TXWY K; RWY 13; HOLD SHORT RWY 25L. THE INSTRUCTIONS WERE READ BACK; AND WE CONTINUED. BECAUSE OF THE SLIGHTLY REDUCED VISIBILITY; MY LACK OF KNOWLEDGE OF THE AIRPORT LAYOUT; THE ATIS CAUTION OF NON-STANDARD HOLD SHORT LINES; AND THAT IT WAS NIGHT; I TAXIED SLOWER THEN NORMAL. AS WE APPROACHED THE END OF RWY 13/31; WE SLOWED MORE TRYING TO IDENTIFY THE HOLD SHORT LINES; WHEN WE ENDED UP AT THE EDGE OF TXWY M; AND RWY 13/31; WE NEVER SAW THE HOLD SHORT LINES; AND BELIEVED THEM TO BE IN FRONT OF US. ATC COMMANDED US TO TAXI UP TXWY M THEN TURN ON RWY 19L AND HOLD SHORT OF RWY 13. ONCE WE WERE SHORT OF RWY 13 WE WERE INFORMED THAT WE MAY HAVE DEVIATED; AND WERE GIVEN A PHONE NUMBER TO COPY DOWN TO CONTACT MKE TRACON UPON REACHING DEST. WE WERE THEN CLEARED AGAIN TO TAXI DOWN RWY 13/31 TO HOLD SHORT OF RWY 25L. THIS TIME THE CONTROLLER INSTRUCTED US TO STOP AS WE APPROACHED THE THRESHOLD FOR RWY 31; THE CONTROLLER THEN STATED THAT THIS IS THE APPROX LOCATION OF THE HOLD SHORT LINE (IT WAS IN FACT THE THRESHOLD; NOT THE HOLD SHORT LINE). NEITHER OF US (MY FO OR MYSELF) COULD SEE ANY INDICATIONS OF A HOLD SHORT LINE AHEAD. ONCE CLEARED BACK ON TO RWY 25L WE TAXIED SLOWLY TRYING TO IDENTIFY THE HOLD SHORT LINES; MY FO THEN NOTICED THE RWY 25L SIGNS AS WE APPROACHED; HOWEVER THEY APPEARED SMALLER AND FARTHER AWAY THAN RWY SIGNS NORMALLY LOOK (THIS WAS PROBABLY DUE TO THE GREATER DISTANCE FROM THE CENTER LINE THEY WERE PLACED; AS WE WERE ON A RWY NOT A TXWY); WE THEN CROSSED THE HOLD SHORT LINES; WHICH RESEMBLED A DARK SMUDGE ACROSS THE RWY; WITH THE YELLOW MARKINGS BARELY VISIBLE UNDER THE ILLUMINATION PROVIDED BY OUR TAXI LIGHT VISIBLE ONLY WHEN WE WERE ACTUALLY CROSSING IT. WE ALMOST MISSED THEM A SECOND TIME DUE TO THE POOR CONDITION THEY ARE IN AND WERE ONLY ABLE TO IDENTIFY THEM FROM FINDING THE RWY IDENT SIGNS THAT WE MISSED THE FIRST TIME AROUND; I THEN NOTED THAT THE HOLD SHORT LINES ARE NOT RECOGNIZABLE AS SUCH. ACFT TAXI LIGHTS WERE ON FOR THE ENTIRE DURATION OF TAXI; AND THE AIRPORT DIAGRAM WAS OPEN; HOWEVER THE INSET THAT DETAILED THE LOCATION OF THE HOLD SHORT LINE WAS BELOW THE AREA LIT BY THE MAP LIGHT. A NEW INSTRUCTION WAS PROVIDED; AND COMPLIED WITH; A CONTACT NUMBER WAS GIVEN; AND CALLED ONCE BLOCKING IN AT DEST. RESTORING PAINTED SURFACES AS TO BE IDENTIFIABLE AT NIGHT; THE ADDITION OF WIGWAG LIGHTS; AT HOT SPOT AREAS MORE CONSPICUOUS SIGNAGE; ALTERNATE PLACEMENT OF THE INSET DISPLAYING THE HS2 AREA.CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: RPTR STATED THAT THE HOLD SHORT LINES FOR RWY 25L; PAINTED ON RWY 13/31; WERE VERY DULL; THE REFLECTIVITY APPEARED TO HAVE BEEN SCRUBBED OFF AND ONLY FRAGMENTS OF THE YELLOW PAINT WERE VISIBLE. IT APPEARED TO HIM THAT THE PAINTED LINE MAY HAVE BEEN REMOVED BY THE ICE AND SNOW REMOVAL EQUIPMENT. THE RPTR STATED THE FLT CREW HAD DISCUSSED THE HOT SPOT DEPICTED ON THE ARPT COMMERCIAL CHART AND WERE AWARE OF THE APPROX POSITION OF THE HOLD LINE; BUT DUE TO THE DARKNESS; MIST AND THE OPTICAL ILLUSION CREATED BY THESE FACTORS; IT WAS VERY DIFFICULT TO SEE THE FADED LINE. ADDITIONALLY; THE RPTR INDICATED THAT THE SIGNAGE FOR THE HOLD LINE WAS DIFFICULT TO SEE AND THE SIGN ON THE LEFT SIDE OF THE ACFT APPEARED TO BE LOW IN THE GND AS IF IN A DITCH. RPTR STATED THAT LARGER SIGNS; A MORE DEFINITIVE LINE AND THE USE OF WIGWAGS WOULD BE A MARKED IMPROVEMENT AND WOULD MORE THAN LIKELY HAVE PREVENTED THE INCIDENT. THE RPTR INDICATED THAT THE HOLD SHORT LINE BEING ON A RWY FOR ANOTHER RWY WAS UNUSUAL AND THAT THE MARKINGS NEED TO BE PROMINENT.