Their arnt any known issues in the Alto. I am a owner my self since October 2019.
What type of intercity travel are you planning to do on it? I have seen several local and imported Altos on my way from Karachi to Lahore on the motorway m5. But personally speaking the car drives wonderfully at speeds 60 and 80 kmph. After that it struggles or you have to rev it hard keeps switching between gears 3 and 5 to maintain rpms above 3000k.
Else at 60-80 the car maintains ideal fuel economy keeping rpms roughly in 2000-3000 range.
If you have a comfortable budget for a Cultus go for Cultus. Alto is perfect for grocery drives, and with the in the city travel. I personally won't recommend this car for heavy usage.
Rest assured even mehrans go upto babusar top so that is a different debate.