There must be something up with your datafile because Maple 10 should be able to handle it no problem. 

With Maple 10, I created 5500 random points and plotted them.  Like this.

with(plots):
a:=[seq(rand(0..90)(),rand(900..3000)(),rand(0..90)()],i=1..5500)]:

pointplot3d(a)

That works fine.  Next I created some random numbers in Excel 3 columns and just selected crtl-c and crtl-v into a notepad file and saved it as sample.txt but renamed it sample.dat to follow your naming convention.  Then read it into Maple like this.

b:=readdata(`c:/test/sample.dat`,3):

nops(b)
               4580

pointplot3d(b)

In that case I only created 4580 pts but that works fine as well.  Perhaps you've already worked it out?  As Tim suggested posting your work even the data file you are pulling the data from will help us better resolve your problem. 

I suspect the problems you are having stem from the way your data file is formatted.  Sometimes if a file contains newline characters or carriage return characters unseen when you open the file, they can cause some havoc on your data when you try to manipulate them after reading them into maple.

Use the concatenation operator

As an example

for i from 1 to 5 do
  f||i;
end do

f1
f2
f3
f4
f5

I too experience the same thing.

Also sometimes pressing enter and it executes but the cursor appears no where, or it just executes into blank space.  I need to use the mouse and point to an area, usually the end of the document somewhere.  But these things seem to only happen after I have deleted some area, I'm backspacing or selecting areas of lines and deleting them. 

I can sometimes get back to normality by going above the problematic area insert a few lines below then go below the problematic area and insert a few lines above and use the mouse to select that area and delete it.  Doesn't always work I still sometimes get a line when I hit return the cursor seems to dissappear. 

Often I can use backspace to delete lines but there's some weird behaviour, I often need to cursor over and use the delete key instead of the backspace. 

In fact you're the first person who's ever brought this issue to attention.  I thought I was the only one experiencing it.  Document mode, yes of course problematic issues in that mode anyways, but that's besides the point.  If I can I will try to document the behaviour and figure out exactly what's happening unless someone else has already.  Sadly I'm in Maple 12 and no updates will be released to fix these older additions, which is unfortunate to say the least.  However I do believe these issues all exist in 13 and 14. 

I'm going to guess your next follow up to this is to find the midpoint of multiple points.  So for some added inspiration you might want to check here http://www.mapleprimes.com/posts/94681-Centroid-Of-A-List-Of-Points

add

axis=[mode=log] to your plot line to change the scale. 

SHIFT+ENTER will enter the next line and not execute the code

And a few other helpfuls

CTRL+SHIFT+K will enter a new line above

CTRL+SHIFT+J will enter a new line below

CTRL+SHIFT+" will allow you to enter directly above a letter

a:=plot(x^2)

op(1,op(1,a)) will produce a list of points used to create the plot

b:=pointplot([[1,2],[3,4],[5,6]]):

op(op(1,b)) will produce the set of points used

c:=spacecurve([sin(x),cos(x),0],x=0..2*Pi):

similarily op(1,op(1,c) for the spacecurve will produce a list of points used. 

As for showing your 3d point you must use plot3d with style=point or use pointplot3d, check the help file

Sometimes that happens when a dvd or cd isn't closed causing compatability drive issues.

for i from 0 to 10 do
  y:=i/2:
  f:=2*x+y:
  a[i]:=plot(f,x,color=COLOR(HUE,i/11):
end do:
plots:-display(seq(a[i],i=0..10))

This is not exactly what you want but it may be helpful.  Here's how we can plot x^2 over the surface cos(x)*x^3

with(plots):with(plottools):

a:=plot3d([cos(x)*x^3],x=-10..10,y=0..100,style=patchnogrid):
b:=plot(x^2):

to3d:=transform((x,y)->[x,y,cos(x)*x^3]):

c:=to3d(b):

display(a,c,axes=box)

f:=x->sin(x)

g:=->2*x

Then it should work

the description: The Fit command fits a model function to data by minimizing the least-squares error. 

Any approximation won't fit all points.  However when I execute your sheet in Maple 12, it doesn't produce the curved line that your graph shows, I produce a straight line. 

and kurve:=plot(g1(59,Q),RangeQ):  actually fits the points better

Is realtime memory usage needed?

To answer one of your questions.  I believe the output plot size has been a request for users for some time.  There have been a few posts asking how to change the size of a plot using code (which would be very nice).

Unless someone has been clever enough to find a way to do it, I think your stuck with standard plot output sizes.

g:=10101110

h:=convert(g,string)

n0:=parse(h[1])
                            n0:=1
n1:=parse(h[2])
                            n1:=0