Yes, the 1.3 patch removed Ultra Terraformers from the game.

It's not that difficult to mod back in if you want to have it, and unlike the other terraforming improvements the computer isn't going to screw up where to place it. It does make individual planets more powerful, but if the computer is taught to specialize its worlds or the player doesn't (fully) specialize their worlds, it's not going to be much more advantageous for the human player than for the computer.

This mod provides repeatable terraforming options, if you're interested.

Alternatively, open NotePad (or another similar program) and paste the following into a new file, then save it to My Documents\My Games\GalCiv3\Mods\(mod name)\Game as RestoredUT.XML:

<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
<DefaultImprovementList
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="../Schema/ImprovementDefs.xsd">
<!-- Created with the Gal Civ 3 Editor -->
<!-- RestoredUT.xml -->

<!-- Begin Improvement -->
 
  <Improvement>
    <InternalName>UltraTerraformer</InternalName>
    <DisplayName>UltraTerraformer_Name</DisplayName>
    <ShortDescription>UltraTerraformer_ShortDec</ShortDescription>
    <Description>UltraTerraformer_Dec</Description>
    <Icon>OmegaTerraforming.png</Icon>
    <BuildIcon>OmegaTerraforming_Build.png</BuildIcon>
    <ListIcon>OmegaTerraforming_Icon.png</ListIcon>
    <ImprovementType>Terraforming</ImprovementType>
    <PlacementType>Terraforming</PlacementType>
    <LandPercentageMin>0.35</LandPercentageMin>
 
    <!-- Stats -->
 
    <Stats>
      <EffectType>ManufacturingCost</EffectType>
      <Scope>Queue</Scope>
      <Target>
        <TargetType>Improvement</TargetType>
      </Target>
      <BonusType>Flat</BonusType>
      <Value>151</Value>
    </Stats>
 
    <!-- Triggers -->
 
    <!-- Level Effect Trigers -->
 
    <!-- Level Effect Stats -->
 
    <!-- Adjacency Bonuses -->

    <!-- Prerequisites -->
 
    <Prerequ>
      <Techs>
        <Option>EnvironmentalResequencing</Option>
      </Techs>
    </Prerequ>
 
  </Improvement>
 
<!-- End Improvement -->

</DefaultImprovementList>

And paste the following into a text file saved as RestoredUTText.XML in My Documents\My Games\GalCiv3\Mods\(mod name)\English\Text:

<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
<StringTableList
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="../../Schema/Lib/StringTable.xsd">
<!-- Created with the Gal Civ 3 Editor -->
<!-- RestoredUTText.xml -->
 
<!-- Tech Names and Descriptions -->
 
  <StringTable>
    <Label>UltraTerraformer_Name</Label>
    <String>Ultra Terraformer</String>
  </StringTable>
 
  <StringTable>
    <Label>UltraTerraformer_ShortDec</Label>
    <String>Terraform all decent unusable land into more decent usable land.</String>
  </StringTable>
 
  <StringTable>
    <Label>UltraTerraformer_Dec</Label>
    <String>Well, the third castle we built on the swamp, now that one's still standing, and that's what you'll inherit - oh shoot, it sank into the swamp. Next!</String>
  </StringTable>

</StringTableList>

Congratulations, you have restored the Ultra Terraformer to your game; it should become available with the tech that gives Biospheres and Resequencers, and will allow you to terraform any tile that could have been terraformed using the first terraforming improvement you unlocked. If you don't want to bother around with adding stuff to \English\Text, just change UltraTerraformer_Name, UltraTerraformer_ShortDec, and UltraTerraformer_Dec to PlanetaryUpgrade_Name, PlanetaryUpgrade_ShortDec, and PlanetaryUpgrade_Dec, and it'll use the name and description of the Soil Enhancement improvement.

Be aware that my instructions are for Win7; if you're using another operating system, you may have to look around a bit to see where the mod goes. You can also implement this by pasting the text provided into ImprovementDefs.XML and ImprovementText.XML, if you'd rather modify core files (which may leave this incompatible with other mods), though if you do this you'll only want the text from <!-- Begin Improvement --> to <!-- End Improvement --> to go into ImprovementDefs.XML and you'll only want the text from the first <StringTable> to the last </StringTable> to go into ImprovementText.XML (and you can skip modifying ImprovementText.XML if you change the descriptions and names as noted earlier). Also be advised that I haven't checked to ensure that the tech I chose for the prerequisite is in all of the tech trees, so there might be a faction that misses out; if there is, then it's just a matter of changing the prerequisite to a common tech (I think TerraformingTech would do it; that's the one that gives the Terraforming improvement).